Question: Low expressed genes
0
gravatar for sana777munquad
4 days ago by
sana777munquad0 wrote:

from one review I found this statement: removing features whose counts are consistently low (for example, removing all features that have a count of less than say 10 in more than 90% of the samples)

Can you explain how to remove less count genes in 90% samples in excel???

Anyone please guide me

rna-seq • 69 views
ADD COMMENTlink modified 4 days ago by ATpoint40k • written 4 days ago by sana777munquad0
2

No, since one should not even consider Excel for NGS datasets. Is R an option?

ADD REPLYlink modified 4 days ago • written 4 days ago by ATpoint40k

ohk then how to remove low count genes in 90% of samples?

ADD REPLYlink written 4 days ago by sana777munquad0
3
gravatar for ATpoint
4 days ago by
ATpoint40k
Germany
ATpoint40k wrote:

Say your matrix is called cts:

keep <- rowSums(cts > 10) > (ncol(cts) * 0.9)
cts[keep,]
ADD COMMENTlink modified 4 days ago • written 4 days ago by ATpoint40k
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