R help - Nov 2011 - readDGE: Error in colnames/length of dimnames not equal to array extent

Hello, all,

I'm a new R user (new to any programming language in general, really), so I
apologize if this is easy/has already been answered (I've attempted
searching online but did not understand the pages I found).

My data is stored in text files with the headers LANE, RNA_NAME, SEQ, and
SEQCNT. I've been using

x = "filename.txt"
y = aggregate(x$SEQCNT, list(x$RNA_NAME), sum)
write.table(y, "C:/path/filename.txt", sep="\t")

to generate an output that I've analyzed using readDGE in the edgeR package:
>RNA Targets = read.delim("Targets.txt", stringsAsFactors = FALSE)
>Targets
Files      Groups
A.txt     1
B.txt     2
>v = readDGE(Targets, skip = 5, comment.char = "!")
I've done this several times; until yesterday, it worked fine. Today,
however, an error message started cropping up after attempting readDGE:

Error in `colnames<-`(`*tmp*`, value = c("1", "2")) : 
  length of 'dimnames' [2] not equal to array extent

I've tried to figure this out with no luck, so absolutely any help would be
appreciated. Thank you all!

--
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Sent from the R help mailing list archive at Nabble.com.

On 11/21/2011 12:43 PM, jazevedo wrote:
> Hello, all,
>
> I'm a new R user (new to any programming language in general, really),
so I
> apologize if this is easy/has already been answered (I've attempted
> searching online but did not understand the pages I found).
>
> My data is stored in text files with the headers LANE, RNA_NAME, SEQ, and
> SEQCNT. I've been using
>
> x = "filename.txt"
> y = aggregate(x$SEQCNT, list(x$RNA_NAME), sum)
> write.table(y, "C:/path/filename.txt", sep="\t")
>
> to generate an output that I've analyzed using readDGE in the edgeR
package:
>
>> RNA Targets = read.delim("Targets.txt", stringsAsFactors =
FALSE)
>> Targets
> Files      Groups
> A.txt     1
> B.txt     2
>> v = readDGE(Targets, skip = 5, comment.char = "!")
>
> I've done this several times; until yesterday, it worked fine. Today,
> however, an error message started cropping up after attempting readDGE:
>
> Error in `colnames<-`(`*tmp*`, value = c("1", "2"))
:
>    length of 'dimnames' [2] not equal to array extent
Hi -- looking at Targets, e.g., summary(Targets), str(Targets), might 
point to input problems. traceback() after the error occurs might point 
to problems in readDGE. Posting to the Bioconductor mailing list

http://bioconductor.org/help/mailing-list/

is appropriate for Bioconductor packages.

Martin
>
> I've tried to figure this out with no luck, so absolutely any help
would be
> appreciated. Thank you all!
>
> --
> View this message in context:
http://r.789695.n4.nabble.com/readDGE-Error-in-colnames-length-of-dimnames-not-equal-to-array-extent-tp4093251p4093251.html
> Sent from the R help mailing list archive at Nabble.com.
>
> ______________________________________________
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> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

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