[BioC] DEXSeq all p-values are 1

[Philip [guest]]

Hello,

I'm trying to use DEXSeq to identify alternative exon usage. Using DESeq I've identified ~200 differentially expressed genes in my gene set. I've basically applied the guidelines from the manual to my data set - single reads in duplicates +/- treatment. I've played around with the parameters in different ways, but no matter how I do it the adjusted p-values all come out as 1 or N/A. The non-adjusted p-values are pretty high, so I reckon the adjusted p-values are "true", however, when I go true single genes I find exons that have really high fold-change values indicating differential expression. Is this a result one can expect (due to e.g. high variance in replicates) or is it possible that something is wrong in my analysis?

Regards,
Philip

 -- output of sessionInfo(): 

R version 2.15.1 (2012-06-22)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
[1] C

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

other attached packages:
[1] DEXSeq_1.4.0        Biobase_2.16.0      BiocGenerics_0.2.0 
[4] BiocInstaller_1.4.9 svMisc_0.9-65       JavaGD_0.5-5       
[7] rJava_0.9-3        

loaded via a namespace (and not attached):
[1] RCurl_1.91-1   XML_3.9-4      biomaRt_2.14.0 hwriter_1.3    plyr_1.7.1    
[6] statmod_1.4.16 stringr_0.6.1 

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