Question: How to plot the batch corrected values in DESeq2
0
gravatar for dhwani.dholakia
9 months ago by
INDIA
dhwani.dholakia0 wrote:

Hello, I have used DESeq2 for differential analysis of small RNA data. I wanted to plot jitter plot of top most differentialy expressed gene using the plotCounts function. When i plot them i can still see the batch effect in the image generated.I then refereed to your post https://support.bioconductor.org/p/76099/. There it is mentioned that it will model the batch effect in linear regression not remove them also in the following threads it is mentioned that we can use limma package removebatcheffect to visualize the batch effect removal. Based on this i have my question as follows:-

Will the batch effect modeled by limma will be same as that by DESeq2 and can that be used as exact proxy or is there any way to extract and plot batch effect removed modeled values

normalization deseq2 • 316 views
ADD COMMENTlink modified 9 months ago by Michael Love25k • written 9 months ago by dhwani.dholakia0
Answer: How to plot the batch corrected values in DESeq2
4
gravatar for Michael Love
9 months ago by
Michael Love25k
United States
Michael Love25k wrote:

The removeBatchEffect() function removes the shifts in mean values. This is not numerically identical to what happens when you include batch in the design of a GLM, but it’s very close, and close enough to be useful for visualization of the counts. You could plot VST data with removeBatchEffect applied and this would represent log2-scale normalized counts with shifts from batch effects removed.

ADD COMMENTlink written 9 months ago by Michael Love25k
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