[BioC] Reading Illumina data from GenomeStudio in limma

[Wei Shi]

Dear Josh,

Could you please provide the command you used and also the first 10 lines of your probe profile file? The read.ilmn function allows any number of columns to be included in your data files. It just extracts those columns whose names match the names specified in the parameters. So I do not know what caused your problem unless I can have a look at your data.


Best regards,

Wei


On Aug 14, 2013, at 12:30 PM, Josh [guest] wrote:

> 
> I have data exported from GenomeStudio (1.6) that I can correctly read and pre-process with lumi. However, when I try using read.ilmn in limma, I found that I get an error saying "Error in `rownames<-`(`*tmp*`, value = list(PROBE_ID = c("ILMN_1762337",  : length of 'dimnames' [1] not equal to array extent." I have found that this was due to the inclusion of extra columns in my probe profiles (TargetID, ProbeID, SPECIES, SOURCE, TRANSCRIPT and on). When I removed them, I can correctly read the probe and control profiles with read.ilmn. Is there a better fix around this than manually removing the columns?
> 
> -- output of sessionInfo(): 
> 
> R version 3.0.0 (2013-04-03)
> Platform: x86_64-apple-darwin10.8.0 (64-bit)
> 
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
> 
> attached base packages:
> [1] parallel  stats     graphics  grDevices utils     datasets  methods   base     
> 
> other attached packages:
> [1] lumi_2.12.0        Biobase_2.20.0     BiocGenerics_0.6.0 limma_3.16.2
> 
> --
> Sent via the guest posting facility at bioconductor.org.
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

______________________________________________________________________
The information in this email is confidential and intend...{{dropped:6}}