error using cqn package
Entering edit mode
Last seen 9 weeks ago

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

 [,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 = rep(500, 590650))

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

Normalization cqn • 181 views
Entering edit mode
Last seen 7 hours ago
United States

There are actually like 30 or so Bioconductor packages that have a function called normalize.quantiles, so it's hard to know which function you are calling. Certainly there isn't any such function in cqn, nor is there anything in the vignette or help pages for cqn that I can find that indicates you should do such a thing as a preliminary step. I am not sure why you are doing that, but it's almost surely a bad idea, and you should stop.

The first argument to cqn is counts, which should be just what it says; a matrix of counts. So try again, using just your 'data' matrix, which should not contain any NA or NaN or Inf values.

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