Help with edgeR

kvk727 · 01-10-2013, 05:50 PM

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!

Gordon Smyth · 01-21-2013, 02:31 PM

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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01-10-2013, 05:50 PM	#1
kvk727 Junior Member Location: Oregon, USA Join Date: Jan 2013 Posts: 2	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!

01-21-2013, 02:31 PM	#2
Gordon Smyth Member Location: Melbourne, Australia Join Date: Apr 2011 Posts: 91	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).