Recalculated abundance data output table with DEseq2
1
0
Entering edit mode
@6662f6a7
Last seen 2 days ago

We are performing larval zebrafish RNAseq using STAR to determine abundances and we can successfully run this data through DEseq2. We would like to know whether it is possible to export a table/matrix from DEseq2 that shows the effects of the dispersion corrections on the original input data (i.e. pre vs post DEseq2 effects on the actual abundance values). Thank you.

DESeq2 • 225 views
0
Entering edit mode
@mikelove
Last seen 1 day ago
United States

I think you mean the size factor scaling?

You can do counts(dds) and counts(dds, normalized=TRUE). See "Access to all calculated values" in the vignette.

0
Entering edit mode

One of the goals of our project is to demonstrate the importance of non-arbitrary data normalization prior to downstream applications with our type of data. Is it possible to get DEseq2 to run the pairwise statistical comparisons on raw, non-normalized abundance counts so we can demonstrate its positive impact?

0
Entering edit mode

Yes, you can get what the LFC and test statistics would be without any accounting for library size via:

sizeFactors(dds) <- rep(1, ncol(dds))
dds <- DESeq(dds)

0
Entering edit mode

Thanks for getting back to me so quickly. The final comparison we are looking to report are the effects of filtering out low count genes using apeglm.

Is there a way to run DEseq2 with no LFCshrink function and output a table? Alternatively can we get the pairwise comparison output files to add columns that display the unshrunk LFC and p-values? Will DEseq2 export a list of all genes that have undergone a given level (i.e. new fold change under 1.5) of shrinkage?

0
Entering edit mode

Yes, DESeq() then results(). When you print the table it will say MLE.

No we don’t have a function to do that.