Question: Filter low expressed genes based on RPKM value
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gravatar for AP
2.6 years ago by
AP20
USA
AP20 wrote:

I have RNA-seq gene expression value for small set of genes in 8 tissues from 28 different individuals. But I have only the RPKM values. Now whats the best way to filter out the low expressed genes from there subset?

rna-seq expression rpkm • 1.9k views
ADD COMMENTlink modified 2.6 years ago by fusion.slope200 • written 2.6 years ago by AP20

That depends on the situation, what is the next step? Filtering genes will not be the end of the analysis, do you plan to do differential expression analysis? What is the experimental design?

ADD REPLYlink written 2.6 years ago by WouterDeCoster37k

Next step will be to do a co-expression and differential expression analysis.

ADD REPLYlink modified 2.6 years ago • written 2.6 years ago by AP20
1

You could also consider to plot the distribution of fold changes to get an idea of what is low and what is highly expressed.

ADD REPLYlink written 2.6 years ago by WouterDeCoster37k

I usually use 1 FPKM as cutoff. This gives the convenience that the log of expression values is always positive making downstream analysis less cumbersome. Definitely arbitrary to take 1 FPKM and values should depend on the situation.

ADD REPLYlink written 2.6 years ago by microfuge1.0k
0
gravatar for fusion.slope
2.6 years ago by
fusion.slope200
fusion.slope200 wrote:

you can use some cutoff like: filter all genes with at least 0.1 rpkm in 90% of your samples. You can play with these values depending on your analysis..

ADD COMMENTlink written 2.6 years ago by fusion.slope200
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