Question: Can I calculate counts from the base mean and log2fc outputs of DESeq2? Also, can I calculate error for counts values from lfcse output?
0
gravatar for robin.uchiyama
3.1 years ago by
robin.uchiyama0 wrote:

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!

chipseq deseq2 error counts log2fc • 649 views
ADD COMMENTlink modified 3.1 years ago by Michael Love24k • written 3.1 years ago by robin.uchiyama0
1

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.

ADD REPLYlink modified 3.1 years ago • written 3.1 years ago by chris86380
Answer: Can I calculate counts from the base mean and log2fc outputs of DESeq2? Also, c
1
gravatar for Michael Love
3.1 years ago by
Michael Love24k
United States
Michael Love24k wrote:

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,...".

ADD COMMENTlink written 3.1 years ago by Michael Love24k
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