Low expressed genes
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7 months ago

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

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

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7 months ago
ATpoint 49k

Say your matrix is called cts:

keep <- rowSums(cts > 10) > (ncol(cts) * 0.9)
cts[keep,]
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