I'm applying cn.mops to ~10 exome sequencing samples. I can apply getSegmentReadCountsFromBAM just fine. But when I try to apply exomecn.mops, I get an error saying that "Some normalization factors are zero! Remove samples or chromosomes for which the average read count is zero, e.g. chromosome Y." I modified my GenomicRanges object so that it excludes chrY. I've also removed any region or sample from my read counts object that contains zero reads on average. But I still get the error message. However, if I remove two of the samples that have a low overall read count, it works fine.

Am I missing something? Or is there some specific criteria I could use to identify samples/regions that should be excluded?

sessionInfo()

R version 3.2.1 (2015-06-18)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.2 LTS

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
[1] magrittr_1.5         dplyr_0.4.2          cn.mops_1.14.1      
[4] GenomicRanges_1.20.5 GenomeInfoDb_1.4.1   IRanges_2.2.5       
[7] S4Vectors_0.6.2      Biobase_2.28.0       BiocGenerics_0.14.0 

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.0       Rsamtools_1.20.4  Biostrings_2.36.1 assertthat_0.1   
 [5] bitops_1.0-6      R6_2.1.0          DBI_0.3.1         zlibbioc_1.14.0  
 [9] XVector_0.8.0     tools_3.2.1 

Hello Stephen,

Thanks for using cn.mops! The default normalization method estimates the size factors based on the median read count per sample. Please do not check the average read counts PER REGION (rows of the read count matrix), but the average read counts PER SAMPLE (columns of the read count matrix).

If one sample has a median read count of 0 (i.e. more than 50% of the regions have zero reads), this might also be an indicator for low sample quality. Especially for exome sequencing this behaviour would be strange.

If the error persists, please send me the read count matrix via email.

Regards,

Günter