Recalculated abundance data output table with DEseq2
1
0
Entering edit mode
@6662f6a7
Last seen 28 days ago
Canada

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 • 281 views
ADD COMMENT
0
Entering edit mode
@mikelove
Last seen 9 hours 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.

ADD COMMENT
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?

ADD REPLY
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)
ADD REPLY
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?

ADD REPLY
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.

ADD REPLY

Login before adding your answer.

Traffic: 327 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6