[BioC] Error creating marrayInfo

[Marcus Davy]

David,
Re: what does the warning mean?

Are they all copies of the same file?

I think the warning is because as scan reads in the list of data it is recycling the elements (number of columns)  in the vector h in the read.marrayRaw code completely scrambling your data.

   dat <- scan(f, quiet = TRUE, what = h, sep = sep, skip = skip + 
                1, quote = quote, ...) 

This could be caused by having just one less/extra tab somewhere in your data files either in your data rows or the colnames header row itself. 

Skip =12331 is a lot of rows to skip is this right?


marcus



Thanks a lot Jean, it works fine now!

I now have another error when reading in my quantarray files using the 
read.marrayRaw function. This is what I do:


> fnames<-dir(path=datadir, pattern ="^[sample]",full.names=TRUE)
> fnames
[1] "C:/ARCHIV~1/R/RW1071~1/library/marrayInput/data/datadir/sample1.tx
t"
[2] "C:/ARCHIV~1/R/RW1071~1/library/marrayInput/data/datadir/sample2.tx
t"
[3] "C:/ARCHIV~1/R/RW1071~1/library/marrayInput/data/datadir/sample3.tx
t"
[4] "C:/ARCHIV~1/R/RW1071~1/library/marrayInput/data/datadir/sample4.tx
t"
[5] "C:/ARCHIV~1/R/RW1071~1/library/marrayInput/data/datadir/sample5.tx
t"
[6] "C:/ARCHIV~1/R/RW1071~1/library/marrayInput/data/datadir/sample6.tx
t"

> mydata.raw<-read.marrayRaw(fnames, path=NULL, name.Gf = "ch2 
Intensity",
+ name.Gb = "ch2 Background", name.Rf = "ch1 Intensity", name.Rb 
= "ch1 Background",
+ layout = mydata.layout, gnames = mydata.names, targets = samples,s
 kip = 12331)
[1] "Reading 
C:/ARCHIV~1/R/RW1071~1/library/marrayInput/data/datadir/sample1.txt"
[1] "Reading 
C:/ARCHIV~1/R/RW1071~1/library/marrayInput/data/datadir/sample2.txt"
[1] "Reading 
C:/ARCHIV~1/R/RW1071~1/library/marrayInput/data/datadir/sample3.txt"
[1] "Reading 
C:/ARCHIV~1/R/RW1071~1/library/marrayInput/data/datadir/sample4.txt"
[1] "Reading 
C:/ARCHIV~1/R/RW1071~1/library/marrayInput/data/datadir/sample5.txt"
[1] "Reading 
C:/ARCHIV~1/R/RW1071~1/library/marrayInput/data/datadir/sample6.txt"
Error in "maTargets<-"(*tmp*, value = targets) : 
        No direct or inherited method for function "maTargets<-" for 
this call
In addition: Warning messages: 
1: number of items read is not a multiple of the number of columns 
2: number of items read is not a multiple of the number of columns 
3: number of items read is not a multiple of the number of columns 
4: number of items read is not a multiple of the number of columns 
5: number of items read is not a multiple of the number of columns 
6: number of items read is not a multiple of the number of columns 
> 

Why do I get this error? and what does the warning mean?
We have each oligonucleotide sequence spotted two times on the chip. 
How does the function handle duplicate spots?

Thanks a lot 

David



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