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Old 01-10-2013, 05:50 PM   #1
kvk727
Junior Member
 
Location: Oregon, USA

Join Date: Jan 2013
Posts: 2
Default Help with edgeR

Hi All,
I am brand new to R (and am completely self taught, perhaps not very well either) and trying to learn how to use edgeR to analyze my RNA sequencing data. I have gotten all the way through the command sets until I reach the following and I get this error;

>detags <-rownames(y)[as.logical(de)]
> plotSmear(lrt,de.tags=detags)
Error in quantile.default(M, c(0.05, 0.95)) :
missing values and NaN's not allowed if 'na.rm' is FALSE

I noticed that in my workspace, the detags value is listed as unknown [0], which I assume is a part of the problem but I have no idea how to fix it, or why it comes up like that.

Any help anyone can offer would be so greatly appreciated!
Cheers!
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Old 01-21-2013, 02:31 PM   #2
Gordon Smyth
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Location: Melbourne, Australia

Join Date: Apr 2011
Posts: 91
Default

See Section 1.3 "How to get help" in the edgeR User's Guide.

You will need to explain in detail how you computed the data objects in your code (y and lrt).
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