Filtering genes with a minimum number of counts between samples
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@a-14337
Last seen 14 days ago
United Kingdom

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!

DESeq2 filtering • 437 views
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@mikelove
Last seen 1 day ago
United States

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.

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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 :)

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