[Bioc-sig-seq] RNASeq, differential expression between group, and large variance within groups

[Laurent Gautier]

Dear List,


We are looking at tag-based RNASeq data, and after running popular 
packages for finding differential expression (edgeR, and DEGseq) we were 
looking that the actual counts for the significant ones.

We are observing a somewhat extreme variance within each group for those 
(say one sample with high count for gene X while others have zero count).

For example, gene X flagged as differentially expressed has the 
following counts (adjusted p-value with DGESeq is 9.401479e-10):
0         grp_A
0         grp_A
0         grp_A
92207  grp_B
0          grp_B
0          grp_B

The underlying binomial is obviously not like the almost-Gaussian 
assumed in microarrays/t-test-like approaches, but this kind of outcome 
is somehow intriguing me. Do people here have experience to share 
regarding how well such gene hold through the qPCR verification step ?



Laurent

PS: In case the sessionInfo() matters

R version 2.12.1 (2010-12-16)
Platform: x86_64-pc-linux-gnu (64-bit)

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

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

other attached packages:
[1] DESeq_1.2.1     locfit_1.5-6    lattice_0.19-17 akima_0.5-4
[5] Biobase_2.10.0

loaded via a namespace (and not attached):
  [1] annotate_1.28.0      AnnotationDbi_1.12.0 DBI_0.2-5
  [4] genefilter_1.32.0    geneplotter_1.28.0   grid_2.12.1
  [7] RColorBrewer_1.0-2   RSQLite_0.9-4        splines_2.12.1
[10] survival_2.36-2      tools_2.12.1         xtable_1.5-6