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Comment: Can I trust the differential expression analysis when the two groups overlap on
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I created a DESeqDataSet object using DESeqDataSetFromMatrix function. I don't anticipate any mismatching or mixup of sampleIDs.
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> so many upregulated genes vs. downregulated, which I think is worrying
Take a look at the plotCounts for a couple of the up-regulated …
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I'm wondering about sample table mixup.
How have you merged your sequencing data with the phenotype data (`colData`)?
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Thanks @mikelove ,
Using vst or rlog doesn't improve the segregation nor is there a remarkable difference when I use 1000 or 2000 most vari…
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I agree that the batch variable should be better modeled as a co-variate than explicit batch correction. There is also RUVm (https://www.nc…
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