[BioC] Question if DESeq can still be used after correction for T0?

[Cor Lieftink [guest]]

We use DESeq for our pooled shRNA screen analysis.  Often this is about comparing a single cell-line for drug treatment (TR) vs untreated (UT) both after a certain number of days, fe. 7.  In this experimental design the transfection on timepoint 0 (T0) is the same for both conditions,  so that when comparing Treated/Untreated one doesnot have to correct for T0, as (TR7/T0) / (UT7/T0) = TR7/UT7. However in case of comparing different cell-lines, the transfection is different, so one need to correct for T0, for example by dividing the counts of both conditions with the counts of T0.  The question is if one can then still use DESeq for differential analysis, perhaps after certain transformations of the data like a log2 transformation of the ratios in order to get a (more) symmetrical distribution? Or what else would be the appropriate statistical test?

Thank your for your reply in advance!

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