Error(s) in re-building vignettes:
--- re-building 'prepare_data.Rmd' using rmarkdown

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

i Using data for tissue: apex
--- finished re-building 'prepare_data.Rmd'

+-+prepare_data.html
--- re-building 'register-data.Rmd' using rmarkdown

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union


-- Information before registration ---------------------------------------------
i Max value of expression_value of all_data_df: 262.28

-- Analysing models for all stretch and shift factor ---------------------------

-- Analysing models for stretch factor = 3 --

\ Calculating score for all shifts (0/10)
| Calculating score for all shifts (1/10)
/ Calculating score for all shifts (5/10)
- Calculating score for all shifts (9/10)
v Calculating score for all shifts (10/10) [7.4s]

\ Normalising expression by mean and sd of compared values (0/10)
| Normalising expression by mean and sd of compared values (0/10)
/ Normalising expression by mean and sd of compared values (1/10)
- Normalising expression by mean and sd of compared values (2/10)
\ Normalising expression by mean and sd of compared values (3/10)
| Normalising expression by mean and sd of compared values (4/10)
/ Normalising expression by mean and sd of compared values (5/10)
- Normalising expression by mean and sd of compared values (6/10)
\ Normalising expression by mean and sd of compared values (7/10)
| Normalising expression by mean and sd of compared values (8/10)
/ Normalising expression by mean and sd of compared values (9/10)
v Normalising expression by mean and sd of compared values (10/10) [177ms]

\ Applying best shift (0/10)
| Applying best shift (0/10)
/ Applying best shift (1/10)
- Applying best shift (2/10)
\ Applying best shift (3/10)
| Applying best shift (4/10)
/ Applying best shift (5/10)
- Applying best shift (6/10)
\ Applying best shift (7/10)
| Applying best shift (8/10)
/ Applying best shift (9/10)
v Applying best shift (10/10) [182ms]

\ Calculating registration vs non-registration comparison AIC & BIC (0/10)
| Calculating registration vs non-registration comparison AIC & BIC (1/10)
/ Calculating registration vs non-registration comparison AIC & BIC (2/10)
- Calculating registration vs non-registration comparison AIC & BIC (3/10)
\ Calculating registration vs non-registration comparison AIC & BIC (4/10)
| Calculating registration vs non-registration comparison AIC & BIC (5/10)
/ Calculating registration vs non-registration comparison AIC & BIC (6/10)
- Calculating registration vs non-registration comparison AIC & BIC (7/10)
\ Calculating registration vs non-registration comparison AIC & BIC (8/10)
| Calculating registration vs non-registration comparison AIC & BIC (9/10)
/ Calculating registration vs non-registration comparison AIC & BIC (10/10)
v Calculating registration vs non-registration comparison AIC & BIC (10/10) [...

v Finished analysing models for stretch factor = 3

-- Analysing models for stretch factor = 2.5 --

\ Calculating score for all shifts (0/10)
| Calculating score for all shifts (2/10)
/ Calculating score for all shifts (6/10)
- Calculating score for all shifts (10/10)
v Calculating score for all shifts (10/10) [7.5s]

\ Normalising expression by mean and sd of compared values (0/10)
| Normalising expression by mean and sd of compared values (0/10)
/ Normalising expression by mean and sd of compared values (1/10)
- Normalising expression by mean and sd of compared values (2/10)
\ Normalising expression by mean and sd of compared values (3/10)
| Normalising expression by mean and sd of compared values (4/10)
/ Normalising expression by mean and sd of compared values (5/10)
- Normalising expression by mean and sd of compared values (6/10)
\ Normalising expression by mean and sd of compared values (7/10)
| Normalising expression by mean and sd of compared values (8/10)
/ Normalising expression by mean and sd of compared values (9/10)
v Normalising expression by mean and sd of compared values (10/10) [193ms]

\ Applying best shift (0/10)
| Applying best shift (0/10)
/ Applying best shift (1/10)
- Applying best shift (2/10)
\ Applying best shift (3/10)
| Applying best shift (4/10)
/ Applying best shift (5/10)
- Applying best shift (6/10)
\ Applying best shift (7/10)
| Applying best shift (8/10)
/ Applying best shift (9/10)
v Applying best shift (10/10) [168ms]

\ Calculating registration vs non-registration comparison AIC & BIC (0/10)
| Calculating registration vs non-registration comparison AIC & BIC (1/10)
/ Calculating registration vs non-registration comparison AIC & BIC (2/10)
- Calculating registration vs non-registration comparison AIC & BIC (3/10)
\ Calculating registration vs non-registration comparison AIC & BIC (4/10)
| Calculating registration vs non-registration comparison AIC & BIC (5/10)
/ Calculating registration vs non-registration comparison AIC & BIC (6/10)
- Calculating registration vs non-registration comparison AIC & BIC (7/10)
\ Calculating registration vs non-registration comparison AIC & BIC (8/10)
| Calculating registration vs non-registration comparison AIC & BIC (9/10)
/ Calculating registration vs non-registration comparison AIC & BIC (10/10)
v Calculating registration vs non-registration comparison AIC & BIC (10/10) [...

v Finished analysing models for stretch factor = 2.5

-- Analysing models for stretch factor = 2 --

\ Calculating score for all shifts (0/10)
| Calculating score for all shifts (2/10)
/ Calculating score for all shifts (6/10)
v Calculating score for all shifts (10/10) [7.5s]

\ Normalising expression by mean and sd of compared values (0/10)
| Normalising expression by mean and sd of compared values (0/10)
/ Normalising expression by mean and sd of compared values (1/10)
- Normalising expression by mean and sd of compared values (2/10)
\ Normalising expression by mean and sd of compared values (3/10)
| Normalising expression by mean and sd of compared values (4/10)
/ Normalising expression by mean and sd of compared values (5/10)
- Normalising expression by mean and sd of compared values (6/10)
\ Normalising expression by mean and sd of compared values (7/10)
| Normalising expression by mean and sd of compared values (8/10)
/ Normalising expression by mean and sd of compared values (9/10)
v Normalising expression by mean and sd of compared values (10/10) [166ms]

\ Applying best shift (0/10)
| Applying best shift (0/10)
/ Applying best shift (1/10)
- Applying best shift (2/10)
\ Applying best shift (3/10)
| Applying best shift (4/10)
/ Applying best shift (5/10)
- Applying best shift (6/10)
\ Applying best shift (7/10)
| Applying best shift (8/10)
/ Applying best shift (9/10)
v Applying best shift (10/10) [171ms]

\ Calculating registration vs non-registration comparison AIC & BIC (0/10)
| Calculating registration vs non-registration comparison AIC & BIC (1/10)
/ Calculating registration vs non-registration comparison AIC & BIC (2/10)
- Calculating registration vs non-registration comparison AIC & BIC (3/10)
\ Calculating registration vs non-registration comparison AIC & BIC (4/10)
| Calculating registration vs non-registration comparison AIC & BIC (5/10)
/ Calculating registration vs non-registration comparison AIC & BIC (6/10)
- Calculating registration vs non-registration comparison AIC & BIC (7/10)
\ Calculating registration vs non-registration comparison AIC & BIC (8/10)
| Calculating registration vs non-registration comparison AIC & BIC (9/10)
/ Calculating registration vs non-registration comparison AIC & BIC (10/10)
v Calculating registration vs non-registration comparison AIC & BIC (10/10) [...

v Finished analysing models for stretch factor = 2

-- Analysing models for stretch factor = 1.5 --

\ Calculating score for all shifts (0/10)
| Calculating score for all shifts (3/10)
/ Calculating score for all shifts (7/10)
v Calculating score for all shifts (10/10) [7.3s]

\ Normalising expression by mean and sd of compared values (0/10)
| Normalising expression by mean and sd of compared values (0/10)
/ Normalising expression by mean and sd of compared values (1/10)
- Normalising expression by mean and sd of compared values (2/10)
\ Normalising expression by mean and sd of compared values (3/10)
| Normalising expression by mean and sd of compared values (4/10)
/ Normalising expression by mean and sd of compared values (5/10)
- Normalising expression by mean and sd of compared values (6/10)
\ Normalising expression by mean and sd of compared values (7/10)
| Normalising expression by mean and sd of compared values (8/10)
/ Normalising expression by mean and sd of compared values (9/10)
v Normalising expression by mean and sd of compared values (10/10) [185ms]

\ Applying best shift (0/10)
| Applying best shift (0/10)
/ Applying best shift (1/10)
- Applying best shift (2/10)
\ Applying best shift (3/10)
| Applying best shift (4/10)
/ Applying best shift (5/10)
- Applying best shift (6/10)
\ Applying best shift (7/10)
| Applying best shift (8/10)
/ Applying best shift (9/10)
v Applying best shift (10/10) [166ms]

\ Calculating registration vs non-registration comparison AIC & BIC (0/10)
| Calculating registration vs non-registration comparison AIC & BIC (1/10)
/ Calculating registration vs non-registration comparison AIC & BIC (2/10)
- Calculating registration vs non-registration comparison AIC & BIC (3/10)
\ Calculating registration vs non-registration comparison AIC & BIC (4/10)
| Calculating registration vs non-registration comparison AIC & BIC (5/10)
/ Calculating registration vs non-registration comparison AIC & BIC (6/10)
- Calculating registration vs non-registration comparison AIC & BIC (7/10)
\ Calculating registration vs non-registration comparison AIC & BIC (8/10)
| Calculating registration vs non-registration comparison AIC & BIC (9/10)
/ Calculating registration vs non-registration comparison AIC & BIC (10/10)
v Calculating registration vs non-registration comparison AIC & BIC (10/10) [...

v Finished analysing models for stretch factor = 1.5

-- Analysing models for stretch factor = 1 --

\ Calculating score for all shifts (0/10)
| Calculating score for all shifts (4/10)
/ Calculating score for all shifts (8/10)
v Calculating score for all shifts (10/10) [7.4s]

\ Normalising expression by mean and sd of compared values (0/10)
| Normalising expression by mean and sd of compared values (0/10)
/ Normalising expression by mean and sd of compared values (1/10)
- Normalising expression by mean and sd of compared values (2/10)
\ Normalising expression by mean and sd of compared values (3/10)
| Normalising expression by mean and sd of compared values (4/10)
/ Normalising expression by mean and sd of compared values (5/10)
- Normalising expression by mean and sd of compared values (6/10)
\ Normalising expression by mean and sd of compared values (7/10)
| Normalising expression by mean and sd of compared values (8/10)
/ Normalising expression by mean and sd of compared values (9/10)
v Normalising expression by mean and sd of compared values (10/10) [173ms]

\ Applying best shift (0/10)
| Applying best shift (0/10)
/ Applying best shift (1/10)
- Applying best shift (2/10)
\ Applying best shift (3/10)
| Applying best shift (4/10)
/ Applying best shift (5/10)
- Applying best shift (6/10)
\ Applying best shift (7/10)
| Applying best shift (8/10)
/ Applying best shift (9/10)
v Applying best shift (10/10) [162ms]

\ Calculating registration vs non-registration comparison AIC & BIC (0/10)
| Calculating registration vs non-registration comparison AIC & BIC (1/10)
/ Calculating registration vs non-registration comparison AIC & BIC (2/10)
- Calculating registration vs non-registration comparison AIC & BIC (3/10)
\ Calculating registration vs non-registration comparison AIC & BIC (4/10)
| Calculating registration vs non-registration comparison AIC & BIC (5/10)
/ Calculating registration vs non-registration comparison AIC & BIC (6/10)
- Calculating registration vs non-registration comparison AIC & BIC (7/10)
\ Calculating registration vs non-registration comparison AIC & BIC (8/10)
| Calculating registration vs non-registration comparison AIC & BIC (9/10)
/ Calculating registration vs non-registration comparison AIC & BIC (10/10)
v Calculating registration vs non-registration comparison AIC & BIC (10/10) [...

v Finished analysing models for stretch factor = 1

-- Model comparison results ----------------------------------------------------
i BIC finds registration better than non-registration for: 10/10

-- Applying the best-shifts and stretches to gene expression -------------------
\ Normalising expression by mean and sd of compared values (0/10)
| Normalising expression by mean and sd of compared values (0/10)
/ Normalising expression by mean and sd of compared values (1/10)
- Normalising expression by mean and sd of compared values (2/10)
\ Normalising expression by mean and sd of compared values (3/10)
| Normalising expression by mean and sd of compared values (4/10)
/ Normalising expression by mean and sd of compared values (5/10)
- Normalising expression by mean and sd of compared values (6/10)
\ Normalising expression by mean and sd of compared values (7/10)
| Normalising expression by mean and sd of compared values (8/10)
/ Normalising expression by mean and sd of compared values (9/10)
v Normalising expression by mean and sd of compared values (10/10) [203ms]

\ Applying best shift (0/10)
| Applying best shift (0/10)
/ Applying best shift (1/10)
- Applying best shift (2/10)
\ Applying best shift (3/10)
| Applying best shift (4/10)
/ Applying best shift (5/10)
- Applying best shift (6/10)
\ Applying best shift (7/10)
| Applying best shift (8/10)
/ Applying best shift (9/10)
v Applying best shift (10/10) [185ms]

i Max value of expression_value: 9.05
\ Imputing transformed expression values (0/10)
| Imputing transformed expression values (0/10)
/ Imputing transformed expression values (1/10)
- Imputing transformed expression values (2/10)
\ Imputing transformed expression values (3/10)
| Imputing transformed expression values (4/10)
/ Imputing transformed expression values (5/10)
- Imputing transformed expression values (6/10)
\ Imputing transformed expression values (7/10)
| Imputing transformed expression values (8/10)
/ Imputing transformed expression values (9/10)
v Imputing transformed expression values (10/10) [493ms]

--- finished re-building 'register-data.Rmd'

--- re-building 'visualise-results.Rmd' using rmarkdown

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union


-- Information before registration ---------------------------------------------
i Max value of expression_value of all_data_df: 262.28

-- Analysing models for all stretch and shift factor ---------------------------

-- Analysing models for stretch factor = 3 --

\ Calculating score for all shifts (0/10)
| Calculating score for all shifts (2/10)
/ Calculating score for all shifts (6/10)
- Calculating score for all shifts (10/10)
v Calculating score for all shifts (10/10) [6.9s]

\ Normalising expression by mean and sd of compared values (0/10)
| Normalising expression by mean and sd of compared values (0/10)
/ Normalising expression by mean and sd of compared values (1/10)
- Normalising expression by mean and sd of compared values (2/10)
\ Normalising expression by mean and sd of compared values (3/10)
| Normalising expression by mean and sd of compared values (4/10)
/ Normalising expression by mean and sd of compared values (5/10)
- Normalising expression by mean and sd of compared values (6/10)
\ Normalising expression by mean and sd of compared values (7/10)
| Normalising expression by mean and sd of compared values (8/10)
/ Normalising expression by mean and sd of compared values (9/10)
v Normalising expression by mean and sd of compared values (10/10) [183ms]

\ Applying best shift (0/10)
| Applying best shift (0/10)
/ Applying best shift (1/10)
- Applying best shift (2/10)
\ Applying best shift (3/10)
| Applying best shift (4/10)
/ Applying best shift (5/10)
- Applying best shift (6/10)
\ Applying best shift (7/10)
| Applying best shift (8/10)
/ Applying best shift (9/10)
v Applying best shift (10/10) [162ms]

\ Calculating registration vs non-registration comparison AIC & BIC (0/10)
| Calculating registration vs non-registration comparison AIC & BIC (1/10)
/ Calculating registration vs non-registration comparison AIC & BIC (2/10)
- Calculating registration vs non-registration comparison AIC & BIC (3/10)
\ Calculating registration vs non-registration comparison AIC & BIC (4/10)
| Calculating registration vs non-registration comparison AIC & BIC (5/10)
/ Calculating registration vs non-registration comparison AIC & BIC (6/10)
- Calculating registration vs non-registration comparison AIC & BIC (7/10)
\ Calculating registration vs non-registration comparison AIC & BIC (8/10)
| Calculating registration vs non-registration comparison AIC & BIC (9/10)
/ Calculating registration vs non-registration comparison AIC & BIC (10/10)
v Calculating registration vs non-registration comparison AIC & BIC (10/10) [...

v Finished analysing models for stretch factor = 3

-- Analysing models for stretch factor = 2.5 --

\ Calculating score for all shifts (0/10)
| Calculating score for all shifts (3/10)
/ Calculating score for all shifts (7/10)
v Calculating score for all shifts (10/10) [7.7s]

\ Normalising expression by mean and sd of compared values (0/10)
| Normalising expression by mean and sd of compared values (0/10)
/ Normalising expression by mean and sd of compared values (1/10)
- Normalising expression by mean and sd of compared values (2/10)
\ Normalising expression by mean and sd of compared values (3/10)
| Normalising expression by mean and sd of compared values (4/10)
/ Normalising expression by mean and sd of compared values (5/10)
- Normalising expression by mean and sd of compared values (6/10)
\ Normalising expression by mean and sd of compared values (7/10)
| Normalising expression by mean and sd of compared values (8/10)
/ Normalising expression by mean and sd of compared values (9/10)
v Normalising expression by mean and sd of compared values (10/10) [178ms]

\ Applying best shift (0/10)
| Applying best shift (0/10)
/ Applying best shift (1/10)
- Applying best shift (2/10)
\ Applying best shift (3/10)
| Applying best shift (4/10)
/ Applying best shift (5/10)
- Applying best shift (6/10)
\ Applying best shift (7/10)
| Applying best shift (8/10)
/ Applying best shift (9/10)
v Applying best shift (10/10) [178ms]

\ Calculating registration vs non-registration comparison AIC & BIC (0/10)
| Calculating registration vs non-registration comparison AIC & BIC (1/10)
/ Calculating registration vs non-registration comparison AIC & BIC (2/10)
- Calculating registration vs non-registration comparison AIC & BIC (3/10)
\ Calculating registration vs non-registration comparison AIC & BIC (4/10)
| Calculating registration vs non-registration comparison AIC & BIC (5/10)
/ Calculating registration vs non-registration comparison AIC & BIC (6/10)
- Calculating registration vs non-registration comparison AIC & BIC (7/10)
\ Calculating registration vs non-registration comparison AIC & BIC (8/10)
| Calculating registration vs non-registration comparison AIC & BIC (9/10)
/ Calculating registration vs non-registration comparison AIC & BIC (10/10)
v Calculating registration vs non-registration comparison AIC & BIC (10/10) [...

v Finished analysing models for stretch factor = 2.5

-- Analysing models for stretch factor = 2 --

\ Calculating score for all shifts (0/10)
| Calculating score for all shifts (3/10)
/ Calculating score for all shifts (7/10)
v Calculating score for all shifts (10/10) [7.8s]

\ Normalising expression by mean and sd of compared values (0/10)
| Normalising expression by mean and sd of compared values (0/10)
/ Normalising expression by mean and sd of compared values (1/10)
- Normalising expression by mean and sd of compared values (2/10)
\ Normalising expression by mean and sd of compared values (3/10)
| Normalising expression by mean and sd of compared values (4/10)
/ Normalising expression by mean and sd of compared values (5/10)
- Normalising expression by mean and sd of compared values (6/10)
\ Normalising expression by mean and sd of compared values (7/10)
| Normalising expression by mean and sd of compared values (8/10)
/ Normalising expression by mean and sd of compared values (9/10)
v Normalising expression by mean and sd of compared values (10/10) [173ms]

\ Applying best shift (0/10)
| Applying best shift (0/10)
/ Applying best shift (1/10)
- Applying best shift (2/10)
\ Applying best shift (3/10)
| Applying best shift (4/10)
/ Applying best shift (5/10)
- Applying best shift (6/10)
\ Applying best shift (7/10)
| Applying best shift (8/10)
/ Applying best shift (9/10)
v Applying best shift (10/10) [171ms]

\ Calculating registration vs non-registration comparison AIC & BIC (0/10)
| Calculating registration vs non-registration comparison AIC & BIC (1/10)
/ Calculating registration vs non-registration comparison AIC & BIC (2/10)
- Calculating registration vs non-registration comparison AIC & BIC (3/10)
\ Calculating registration vs non-registration comparison AIC & BIC (4/10)
| Calculating registration vs non-registration comparison AIC & BIC (5/10)
/ Calculating registration vs non-registration comparison AIC & BIC (6/10)
- Calculating registration vs non-registration comparison AIC & BIC (7/10)
\ Calculating registration vs non-registration comparison AIC & BIC (8/10)
| Calculating registration vs non-registration comparison AIC & BIC (9/10)
/ Calculating registration vs non-registration comparison AIC & BIC (10/10)
v Calculating registration vs non-registration comparison AIC & BIC (10/10) [...

v Finished analysing models for stretch factor = 2

-- Analysing models for stretch factor = 1.5 --

\ Calculating score for all shifts (0/10)
| Calculating score for all shifts (4/10)
/ Calculating score for all shifts (8/10)
v Calculating score for all shifts (10/10) [7.3s]

\ Normalising expression by mean and sd of compared values (0/10)
| Normalising expression by mean and sd of compared values (0/10)
/ Normalising expression by mean and sd of compared values (1/10)
- Normalising expression by mean and sd of compared values (2/10)
\ Normalising expression by mean and sd of compared values (3/10)
| Normalising expression by mean and sd of compared values (4/10)
/ Normalising expression by mean and sd of compared values (5/10)
- Normalising expression by mean and sd of compared values (6/10)
\ Normalising expression by mean and sd of compared values (7/10)
| Normalising expression by mean and sd of compared values (8/10)
/ Normalising expression by mean and sd of compared values (9/10)
v Normalising expression by mean and sd of compared values (10/10) [177ms]

\ Applying best shift (0/10)
| Applying best shift (0/10)
/ Applying best shift (1/10)
- Applying best shift (2/10)
\ Applying best shift (3/10)
| Applying best shift (4/10)
/ Applying best shift (5/10)
- Applying best shift (6/10)
\ Applying best shift (7/10)
| Applying best shift (8/10)
/ Applying best shift (9/10)
v Applying best shift (10/10) [164ms]

\ Calculating registration vs non-registration comparison AIC & BIC (0/10)
| Calculating registration vs non-registration comparison AIC & BIC (1/10)
/ Calculating registration vs non-registration comparison AIC & BIC (2/10)
- Calculating registration vs non-registration comparison AIC & BIC (3/10)
\ Calculating registration vs non-registration comparison AIC & BIC (4/10)
| Calculating registration vs non-registration comparison AIC & BIC (5/10)
/ Calculating registration vs non-registration comparison AIC & BIC (6/10)
- Calculating registration vs non-registration comparison AIC & BIC (7/10)
\ Calculating registration vs non-registration comparison AIC & BIC (8/10)
| Calculating registration vs non-registration comparison AIC & BIC (9/10)
/ Calculating registration vs non-registration comparison AIC & BIC (10/10)
v Calculating registration vs non-registration comparison AIC & BIC (10/10) [...

v Finished analysing models for stretch factor = 1.5

-- Analysing models for stretch factor = 1 --

\ Calculating score for all shifts (0/10)
| Calculating score for all shifts (1/10)
/ Calculating score for all shifts (5/10)
- Calculating score for all shifts (9/10)
v Calculating score for all shifts (10/10) [7.6s]

\ Normalising expression by mean and sd of compared values (0/10)
| Normalising expression by mean and sd of compared values (0/10)
/ Normalising expression by mean and sd of compared values (1/10)
- Normalising expression by mean and sd of compared values (2/10)
\ Normalising expression by mean and sd of compared values (3/10)
| Normalising expression by mean and sd of compared values (4/10)
/ Normalising expression by mean and sd of compared values (5/10)
- Normalising expression by mean and sd of compared values (6/10)
\ Normalising expression by mean and sd of compared values (7/10)
| Normalising expression by mean and sd of compared values (8/10)
/ Normalising expression by mean and sd of compared values (9/10)
v Normalising expression by mean and sd of compared values (10/10) [174ms]

\ Applying best shift (0/10)
| Applying best shift (0/10)
/ Applying best shift (1/10)
- Applying best shift (2/10)
\ Applying best shift (3/10)
| Applying best shift (4/10)
/ Applying best shift (5/10)
- Applying best shift (6/10)
\ Applying best shift (7/10)
| Applying best shift (8/10)
/ Applying best shift (9/10)
v Applying best shift (10/10) [166ms]

\ Calculating registration vs non-registration comparison AIC & BIC (0/10)
| Calculating registration vs non-registration comparison AIC & BIC (1/10)
/ Calculating registration vs non-registration comparison AIC & BIC (2/10)
- Calculating registration vs non-registration comparison AIC & BIC (3/10)
\ Calculating registration vs non-registration comparison AIC & BIC (4/10)
| Calculating registration vs non-registration comparison AIC & BIC (5/10)
/ Calculating registration vs non-registration comparison AIC & BIC (6/10)
- Calculating registration vs non-registration comparison AIC & BIC (7/10)
\ Calculating registration vs non-registration comparison AIC & BIC (8/10)
| Calculating registration vs non-registration comparison AIC & BIC (9/10)
/ Calculating registration vs non-registration comparison AIC & BIC (10/10)
v Calculating registration vs non-registration comparison AIC & BIC (10/10) [...

v Finished analysing models for stretch factor = 1

-- Model comparison results ----------------------------------------------------
i BIC finds registration better than non-registration for: 10/10

-- Applying the best-shifts and stretches to gene expression -------------------
\ Normalising expression by mean and sd of compared values (0/10)
| Normalising expression by mean and sd of compared values (0/10)
/ Normalising expression by mean and sd of compared values (1/10)
- Normalising expression by mean and sd of compared values (2/10)
\ Normalising expression by mean and sd of compared values (3/10)
| Normalising expression by mean and sd of compared values (4/10)
/ Normalising expression by mean and sd of compared values (5/10)
- Normalising expression by mean and sd of compared values (6/10)
\ Normalising expression by mean and sd of compared values (7/10)
| Normalising expression by mean and sd of compared values (8/10)
/ Normalising expression by mean and sd of compared values (9/10)
v Normalising expression by mean and sd of compared values (10/10) [178ms]

\ Applying best shift (0/10)
| Applying best shift (0/10)
/ Applying best shift (1/10)
- Applying best shift (2/10)
\ Applying best shift (3/10)
| Applying best shift (4/10)
/ Applying best shift (5/10)
- Applying best shift (6/10)
\ Applying best shift (7/10)
| Applying best shift (8/10)
/ Applying best shift (9/10)
v Applying best shift (10/10) [171ms]

i Max value of expression_value: 9.05
\ Imputing transformed expression values (0/10)
| Imputing transformed expression values (0/10)
/ Imputing transformed expression values (1/10)
- Imputing transformed expression values (2/10)
\ Imputing transformed expression values (3/10)
| Imputing transformed expression values (4/10)
/ Imputing transformed expression values (5/10)
- Imputing transformed expression values (6/10)
\ Imputing transformed expression values (7/10)
| Imputing transformed expression values (8/10)
/ Imputing transformed expression values (9/10)
v Imputing transformed expression values (10/10) [465ms]

Warning: Removed 84 rows containing missing values (geom_point).
Warning: Removed 4 row(s) containing missing values (geom_path).
Warning: Removed 28 rows containing missing values (geom_point).
Warning: Removed 4 row(s) containing missing values (geom_path).
--- finished re-building 'visualise-results.Rmd'

SUMMARY: processing the following file failed:
  'prepare_data.Rmd'

Error: Vignette re-building failed.
Execution halted