Question: Deseq2 count matrix
0
gravatar for Sam
2.0 years ago by
Sam130
Sam130 wrote:

Hi all

I have raw reads matrix for miRNAs expression and I want complete the differential expression analysis with DESeq2, how I can exclude reads with average reads below 1 (average reads of biological replicates) from count matrix before analysis with Deseq2 ?

Thanks

rna-seq deseq2 R • 1.3k views
ADD COMMENTlink modified 22 months ago by Biostar ♦♦ 20 • written 2.0 years ago by Sam130
3

You do not need to. DESeq2 has an internal data-driven function to exclude low counts. There are many questions/posts about this topic on Bioconductor, just google around a bit.

ADD REPLYlink modified 2.0 years ago • written 2.0 years ago by ATpoint24k

is it also exclude samples have zero counts ? I find this comment in bioconductor for NA p-value

"Note on p-values set to NA: some values in the results table can be set to NA for one of the following reasons:

If within a row, all samples have zero counts, the baseMean column will be zero, and the log2 fold change estimates, p value and adjusted p value will all be set to NA."

ADD REPLYlink modified 2.0 years ago • written 2.0 years ago by Sam130
1

You will have to specifically remove transcripts with 0 counts, as DESeq2 will leave these in the dataset and not do anything with them. Take a look at Michael Love's answer here: https://support.bioconductor.org/p/64153/

If you want to filter your results() object from DEseq2, then take a look at Michael Love's answer here: https://support.bioconductor.org/p/96219/

ADD REPLYlink modified 2.0 years ago • written 2.0 years ago by Kevin Blighe49k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 789 users visited in the last hour