Can I calculate counts from the base mean and log2fc outputs of DESeq2? Also, can I calculate error for counts values from lfcse output?
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@robinuchiyama-10844
Last seen 5.3 years ago

Hi Bioconductor community,

I performed a categorical analysis (control vs treated) using DESeq2, and I want to put together a figure where I show the average counts in the control and treated groups that includes error and a p value.  To calculate counts of the treated group, do I simply multiply the log2 fc value (after first taking the anti-log2) by the base mean value (which is representative of control counts)?  Do the standard error and adjusted p values only apply to the fc or can it be applied to counts?

Thanks!

deseq2 chipseq counts log2fc error • 929 views
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There will be better replies I am sure, but I would just script that in R yourself i.e. calculation of mean counts for condition 1 versus 2 and standard error/ deviation whatever - it is a quick job even if you are a beginner. You just need to export the normalised counts from DESEQ then work from that. Then I am sure the p values apply to the counts because the fold change is calculated from the counts.

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@mikelove
Last seen 2 hours ago
United States

Take a look at the plotCounts function which is shown in the vignette. Rather than showing a summary (mean + SE) it's much preferred to just show the normalized counts themselves. If you have many samples (n > 20) you could also use a boxplot to summarize the normalized counts across groups. This is easily done with ggplot2, see the section of the vignette "Plot counts" that starts "For customized plotting,...".

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