Question: Filtering values for two group separately
0
gravatar for Expert
21 months ago by
Expert0
Expert0 wrote:

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 • 466 views
ADD COMMENTlink modified 21 months ago by kristoffer.vittingseerup3.4k • written 21 months ago by Expert0
1

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

ADD REPLYlink written 21 months ago by Asaf8.5k
1

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 REPLYlink written 21 months ago by WouterDeCoster44k
1
gravatar for kristoffer.vittingseerup
21 months ago by
European Union
kristoffer.vittingseerup3.4k wrote:

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 COMMENTlink written 21 months ago by kristoffer.vittingseerup3.4k

You should probably not filter at all

ADD REPLYlink written 21 months ago by Asaf8.5k
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