Entering edit mode
4.0 years ago
pt.taklifi
▴
60
Hello everyone . I have a count matrix of sequencing data showing how many fragments there is in each region here is a few rows of my data
head(data[,1:6])
[,1] [,2] [,3] [,4] [,5] [,6]
1 3 6 0 0 3 1
2 4 4 0 0 0 0
3 4 4 1 0 2 2
4 0 2 0 0 0 0
5 0 1 0 0 0 0
6 0 5 2 0 0 0
I am trying to GC content normalize my data first I did a quantile normalization with normalize.quantiles function and named output data.norm.
then I calculated GC content for each region .Finally using cqn
i tried to do GC content normalization
cqn( data.norm, x=gc ,lengths = l)
but I get the following error
Error in qr.default(t(const)) :
NA/NaN/Inf in foreign function call (arg 1)
I'm not familiar with cqn package so I don't exactly know what is the problem here