[BioC] edgeR GLM to adjust for batch effect

[Ryan C. Thompson]

You don't necessarily need every condition in every batch for the 
comparison to be effective, but having only one batch in common is not 
good. If I understand correctly, batch 3 would be the dominant 
contributor to the estimates of fold changes in the comparisons that you 
care about, since any other change would be mostly absorbed into the 
batch effects. I think the first step you should take is to fit the full 
model with conditions and batch effect and find out whether the batch 
effects appear to be significant enough to warrant inclusion in the 
model, and if not, then drop them.

-Ryan

On Wed 26 Mar 2014 03:47:42 PM PDT, Ryan Basom [guest] wrote:
>
>
> 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
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
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