[BioC] edgeR GLM to adjust for batch effect

[Ryan Basom [guest]]

Hi,

I'd like to use a GLM in edgeR to adjust for a batch effect, though only one of my four batches has samples from both groups in the comparisons that I'd like to conduct (pos-nc & neg-nc):

         1 2 3 4
pos      3 5 9 0
neg      5 4 7 0
nc       0 0 5 8

I suspect that using a GLM in edgeR to adjust for batch will only work properly if there's representation of both groups from a given comparison in every batch, though would like to know if this is otherwise.  I see a batch effect using PVCA on just the pos and neg samples, and would like to try to adjust for it somehow.  Please advise. 

Thanks,
Ryan






 -- output of sessionInfo(): 

R version 3.0.3 (2014-03-06)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               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    LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
 [1] pvca_1.2.0                 beadChipCoreTools_0.49     beadAnno_1.0               lumi_2.14.1               
 [5] Biobase_2.22.0             BiocGenerics_0.8.0         genefilter_1.44.0          arrayQualityMetrics_3.18.0
 [9] edgeR_3.4.2                limma_3.18.12             

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