Question: DESeq2 comparison of normalized counts from different experiments
0
gravatar for Matthias
8 months ago by
Matthias10
Matthias10 wrote:

Hi,

I'm putting together a database to compare gene expression across many different RNA-seq experiments. I have multiple DESeq2 normalized counts matrices from the different experiments.

My question is am I able to merge these normalized counts matrices by gene names and directly compare the gene expression across all of these experiments? Or will I have to re-run DESeq2 with all samples together to have the normalization done together?

Thanks, Matt

rna-seq deseq2 • 306 views
ADD COMMENTlink written 8 months ago by Matthias10

The DeSeq2 normalizes counts with respect to library size. So in principal it should be able to compare different sequencing runs together even with different library sizes.

ADD REPLYlink written 8 months ago by piyushjo110
4
gravatar for jared.andrews07
8 months ago by
jared.andrews072.3k
St. Louis, MO
jared.andrews072.3k wrote:

You'll want to run them all together, otherwise the gene-dispersion estimates won't be accurate, meaning your counts won't be comparable across experiments. You'll likely still run into batch effects, but at least you can try to account for those.

ADD COMMENTlink written 8 months ago by jared.andrews072.3k
1

Moved your comment to an answer, jared.

ADD REPLYlink written 8 months ago by Kevin Blighe42k
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