[BioC] DEXSEq warning when using TRT functions

[Eva Benito [guest]]

Dear list, 

My name is Eva Benito, I'm trying to implement DEXSeq for my RNASeq data. I aligned with tophat2 and counted with the corresponding scripts for dexseq in HTSeq. No problems there. Then I read the data into R and because I have quite some samples (18), I decided to give the TRT version of the DEXSeq functions a try, since they were specifically designed to optimize running time for a large number of samples (as I found them in this post here: https://stat.ethz.ch/pipermail/bioconductor/2013-January/050252.html). 

I keep getting a warning after I fit the dispersion function (see below) which does not appear when I run the regular version of estimateDispersions() and I'm wondering whether there's something I'm missing and whether there's something wrong with this. I found these two posts (https://stat.ethz.ch/pipermail/bioconductor/2012-February/043644.html and http://grokbase.com/t/r/bioconductor/11bx58k9hk/bioc-error-in-dexseq-fitdispersionfunction) and it seems that back then the solution was to update DEXSeq to the newest version, but I am running the latest version as far as I know and I even installed the development version and still got the warning.  

Any input in this respect would be greatly appreciated!


Thanks a lot in advance and best regards, 

  Eva

Here's the warning I get: 

> subset = fitDispersionFunction(subset)
Warning messages:
1: In glmgam.fit(mm, disps[good], coef.start = coefs) :
  Too much damping - convergence tolerance not achievable
2: In glmgam.fit(mm, disps[good], coef.start = coefs) :
  Too much damping - convergence tolerance not achievable


Here's the code I'm using: 

library(DEXSeq)
library(parallel)

files = list.files(pattern = 'CA_[0-9]')

metadata = read.delim('metadata_CA.txt', stringsAsFactors = TRUE)

cds.exons = read.HTSeqCounts(files, metadata, flattenedfile = '/usr/users/ebenito/mm9_ensembl_dexseq.gff')

subset = cds.exons[1:1000,]
subset = estimateSizeFactors(subset)
subset = estimateDispersionsTRT(subset)
subset = fitDispersionFunction(subset)
subset = testForDEUTRT(subset)
res = DEUresultTable(subset)

And here's the sessionInfo():

R version 3.0.1 (2013-05-16)
Platform: x86_64-unknown-linux-gnu (64-bit)

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=C                 LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] DEXSeq_1.7.3       Biobase_2.20.0     BiocGenerics_0.6.0

loaded via a namespace (and not attached):
 [1] biomaRt_2.16.0       Biostrings_2.28.0    bitops_1.0-5        
 [4] GenomicRanges_1.12.4 hwriter_1.3          IRanges_1.18.1      
 [7] RCurl_1.95-4.1       Rsamtools_1.12.3     statmod_1.4.17      
[10] stats4_3.0.1         stringr_0.6.2        XML_3.98-1.1        
[13] zlibbioc_1.2.0   

 -- output of sessionInfo(): 

R version 3.0.1 (2013-05-16)
Platform: x86_64-unknown-linux-gnu (64-bit)

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=C                 LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] DEXSeq_1.7.3       Biobase_2.20.0     BiocGenerics_0.6.0

loaded via a namespace (and not attached):
 [1] biomaRt_2.16.0       Biostrings_2.28.0    bitops_1.0-5        
 [4] GenomicRanges_1.12.4 hwriter_1.3          IRanges_1.18.1      
 [7] RCurl_1.95-4.1       Rsamtools_1.12.3     statmod_1.4.17      
[10] stats4_3.0.1         stringr_0.6.2        XML_3.98-1.1        
[13] zlibbioc_1.2.0   

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