Filtering values for two group separately
1
0
Entering edit mode
2.4 years ago
Expert ▴ 10

There are 6 controls and 6 treatment variables in a dataset. I used these command first:

mydata <- read.delim(".csv", header = TRUE, sep=",", stringsAsFactors = FALSE, row.names = 1)   
targets <- data.frame(fileName=colnames(mydata)[1:12], Group=rep(c("Control" , "Treatment"), each= 6))

I want to filter for remove low counts, But in the same table this filtering will be:

control of %20 <1 , treatment of %20 <1 separately.

I could not filter in the same table.

Can you help me? Thank you.

RNA-Seq • 576 views
ADD COMMENT
1
Entering edit mode

A. You won't get a reply when people don't understand what you're asking B. Don't use FPKM

ADD REPLY
1
Entering edit mode

How is at least twenty percent of each group is filtered to be greater than zero? That is 20% of the control group and 20% of the treatment group separately.

That sentence as it is written doesn't make sense at all. Please elaborate, and it may be helpful to include examples.

ADD REPLY
1
Entering edit mode
2.4 years ago

You should not filter individually in each group! Filtering in individual groups will inflate the false positive rate on any statistics you do downstream of the filtering.

ADD COMMENT
0
Entering edit mode

You should probably not filter at all

ADD REPLY

Login before adding your answer.

Traffic: 2097 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6