Discordant analysis with 5 components does not return 25 classes.

[gaiatek]

Hi, when trying to run a discordant analysis with 5 components on a sample datasets (20 proteins, 145 samples), the resulting probMatrix has only 16 columns (as opposed to the 25 possibilities). I also get multiple columns containing all 0 in the probMatrix. Depending on the subset of samples that I use either V14 or V6,V8,V10,V13 and V14 all have zeroes. These results seem at best unreliable.

So I used a similar approach using the data from the vignette, and was not able to run a successful analysis. Using the code below:

# Trying with example data from vignette
data(TCGA_GBM_transcript_microarray)
groups <- c(rep(1,10), rep(2,20)) # fixed from vignette

wthn_vectors <- createVectors(TCGA_GBM_transcript_microarray, groups = groups)
wthn_result <- discordantRun(wthn_vectors$v1, wthn_vectors$v2,
                             TCGA_GBM_transcript_microarray,
                             components = 5)

simply crashes R with following error message " This application has requested the Runtime to terminate it in an unusual way. Please contact the application's support team for more information." which is something that I have never seen in 10 years of using R...

Here is my session info:

> session_info()
Session info -----------------------------------------------------------------
 setting  value                       
 version  R version 3.4.1 (2017-06-30)
 system   x86_64, mingw32             
 ui       RStudio (1.0.153)           
 language (EN)                        
 collate  English_United States.1252  
 tz       America/New_York            
 date     2017-08-07                  

Packages ---------------------------------------------------------------------
 package      * version date       source        
 assertthat     0.2.0   2017-04-11 CRAN (R 3.4.1)
 base         * 3.4.1   2017-06-30 local         
 bindr          0.1     2016-11-13 CRAN (R 3.4.1)
 bindrcpp       0.2     2017-06-17 CRAN (R 3.4.1)
 Biobase      * 2.36.2  2017-05-04 Bioconductor  
 BiocGenerics * 0.22.0  2017-04-25 Bioconductor  
 biwt           1.0     2012-10-29 CRAN (R 3.4.1)
 broom          0.4.2   2017-02-13 CRAN (R 3.4.0)
 cellranger     1.1.0   2016-07-27 CRAN (R 3.4.1)
 cluster        2.0.6   2017-03-10 CRAN (R 3.4.1)
 colorspace     1.3-2   2016-12-14 CRAN (R 3.4.1)
 compiler       3.4.1   2017-06-30 local         
 datasets     * 3.4.1   2017-06-30 local         
 DEoptimR       1.0-8   2016-11-19 CRAN (R 3.4.0)
 devtools     * 1.13.3  2017-08-02 CRAN (R 3.4.1)
 digest         0.6.12  2017-01-27 CRAN (R 3.4.1)
 discordant   * 1.0.0   2017-04-25 Bioconductor  
 dplyr        * 0.7.2   2017-07-20 CRAN (R 3.4.1)
 forcats        0.2.0   2017-01-23 CRAN (R 3.4.1)
 foreign        0.8-69  2017-06-22 CRAN (R 3.4.1)
 ggplot2      * 2.2.1   2016-12-30 CRAN (R 3.4.1)
 glue           1.1.1   2017-06-21 CRAN (R 3.4.1)
 graphics     * 3.4.1   2017-06-30 local         
 grDevices    * 3.4.1   2017-06-30 local         
 grid           3.4.1   2017-06-30 local         
 gtable         0.2.0   2016-02-26 CRAN (R 3.4.1)
 gtools         3.5.0   2015-05-29 CRAN (R 3.4.0)
 haven          1.1.0   2017-07-09 CRAN (R 3.4.1)
 hms            0.3     2016-11-22 CRAN (R 3.4.1)
 httr           1.2.1   2016-07-03 CRAN (R 3.4.1)
 jsonlite       1.5     2017-06-01 CRAN (R 3.4.1)
 lattice        0.20-35 2017-03-25 CRAN (R 3.4.1)
 lazyeval       0.2.0   2016-06-12 CRAN (R 3.4.1)
 lubridate      1.6.0   2016-09-13 CRAN (R 3.4.1)
 magrittr       1.5     2014-11-22 CRAN (R 3.4.1)
 MASS           7.3-47  2017-02-26 CRAN (R 3.4.1)
 memoise        1.1.0   2017-04-21 CRAN (R 3.4.1)
 methods      * 3.4.1   2017-06-30 local         
 mnormt         1.5-5   2016-10-15 CRAN (R 3.4.0)
 modelr         0.1.1   2017-07-24 CRAN (R 3.4.1)
 munsell        0.4.3   2016-02-13 CRAN (R 3.4.1)
 mvtnorm        1.0-6   2017-03-02 CRAN (R 3.4.0)
 nlme           3.1-131 2017-02-06 CRAN (R 3.4.1)
 parallel     * 3.4.1   2017-06-30 local         
 pcaPP          1.9-72  2017-06-27 CRAN (R 3.4.0)
 pkgconfig      2.0.1   2017-03-21 CRAN (R 3.4.1)
 plyr           1.8.4   2016-06-08 CRAN (R 3.4.1)
 psych          1.7.5   2017-05-03 CRAN (R 3.4.1)
 purrr        * 0.2.2.2 2017-05-11 CRAN (R 3.4.1)
 R6             2.2.2   2017-06-17 CRAN (R 3.4.1)
 Rcpp           0.12.12 2017-07-15 CRAN (R 3.4.1)
 readr        * 1.1.1   2017-05-16 CRAN (R 3.4.1)
 readxl         1.0.0   2017-04-18 CRAN (R 3.4.1)
 reshape2       1.4.2   2016-10-22 CRAN (R 3.4.1)
 rlang          0.1.1   2017-05-18 CRAN (R 3.4.1)
 robustbase     0.92-7  2016-12-09 CRAN (R 3.4.1)
 rrcov          1.4-3   2016-09-06 CRAN (R 3.4.1)
 rvest          0.3.2   2016-06-17 CRAN (R 3.4.1)
 scales         0.4.1   2016-11-09 CRAN (R 3.4.1)
 stats        * 3.4.1   2017-06-30 local         
 stats4         3.4.1   2017-06-30 local         
 stringi        1.1.5   2017-04-07 CRAN (R 3.4.0)
 stringr        1.2.0   2017-02-18 CRAN (R 3.4.1)
 tibble       * 1.3.3   2017-05-28 CRAN (R 3.4.1)
 tidyr        * 0.6.3   2017-05-15 CRAN (R 3.4.1)
 tidyverse    * 1.1.1   2017-01-27 CRAN (R 3.4.1)
 tools          3.4.1   2017-06-30 local         
 utils        * 3.4.1   2017-06-30 local         
 withr          2.0.0   2017-07-28 CRAN (R 3.4.1)
 xml2           1.1.1   2017-01-24 CRAN (R 3.4.1)

Thanks!