Question: Filtering genes with a minimum number of counts between samples
gravatar for A
8 months ago by
A0 wrote:

Hi all, 

I have searched for this high and low with no luck. I was wondering if it is possible (over a time course experiment) to filter genes that have a specific change across the time points. 

So for example, I would like to be able to look at genes that change from one time point to another only if it has a difference of a minimum change of 50 counts or more.  So if the change from one gene to another were 45 counts (for example), it would be rejected. Is there any way of doing this pre/post DDS and if so, would somebody be kind enough to share some code for this?


Many thanks!

ADD COMMENTlink modified 8 months ago by Michael Love19k • written 8 months ago by A0
gravatar for Michael Love
8 months ago by
Michael Love19k
United States
Michael Love19k wrote:

In DESeq2, there is not a concept of filtering by absolute number of counts, instead we compute the fold change. You can specify a minimum fold change. See the vignette section about lfcThreshold.

ADD COMMENTlink written 8 months ago by Michael Love19k

Thank you for the reply! I will look into setting a minimum fold change but will also look at defining this using a base r function with the count matrix after DESeq.

Thanks once again :)

ADD REPLYlink written 8 months ago by A0
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