Question

Low expressed genes

0

Entering edit mode

3.5 years ago

sana777munquad ▴ 10

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 • 748 views

ADD COMMENT • link updated 3.5 years ago by ATpoint 81k • written 3.5 years ago by sana777munquad ▴ 10

2

Entering edit mode

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

ADD REPLY • link 3.5 years ago by ATpoint 81k

0

Entering edit mode

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

ADD REPLY • link 3.5 years ago by sana777munquad ▴ 10

score 3 · Answer 1 · 2020-10-15

3

Entering edit mode

3.5 years ago

ATpoint 81k

Say your matrix is called cts:

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

ADD COMMENT • link 3.5 years ago by ATpoint 81k