[BioC] read.ilmn error: length of 'dimnames' [1] not equal to array extent

[Wei Shi]

Dear Mark,

Could you provide the commands you used for reading the data and also session info? It will also be helpful to dissect the problem if you could provide the first 10 lines of your sample data.

Cheers,

Wei

On Nov 17, 2012, at 6:16 AM, Mark Ebbert wrote:

> Hi,
> 
> This is my first time analyzing Illumina microarray data, so I'm not familiar with the data format as exported by BeadStudio or GenomeStudio. The problem is that I can't get read.ilmn to read in either the sample data or the control data. The error I get when reading in the sample data alone is as follows:
> 
> Error in `rownames<-`(`*tmp*`, value = list(PROBE_ID = c("ILMN_2896528",  : 
>  length of 'dimnames' [1] not equal to array extent
> 
> When reading in the control data I get the following error:
> 
> Error in readGenericHeader(fname, columns = expr) : 
>  Specified column headings not found in file
> 
> This data comes from the Genome Technology Access Center at WashU and they claim the data is directly exported from GenomeStudio.
> 
> Could it be from unexpected characters in the file (e.g. R doesn't like #, -, and other characters in certain situations)? There aren't any #'s in the file, but I'm curious is read.ilmn handles these cases. The sample names do have '-' in the name, but I tried removing those and it didn't make a difference.
> 
> I appreciate your help!
> 
> Mark
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