[BioC] Error using Ringos readNimblegen

[Joern Toedling]

Hi Morten,
sorry for the trouble, my first guess would be that the raw data pair 
files are of some unexpected format, possibly having no column named 
"PM". I would be very grateful, if you could send me the first few lines 
of one of those pair files off-list, so that I can have a more detailed 
look and extend the function 'readNgIntensitiesTxt' to handle that 
format as well.
Btw, I advise you to update your R and Bioconductor to the current 
release version (R 2.7.0 and BioC 2.2, released 1 May). Since you are 
using Linux, you are also very welcome to use the current development 
version of Ringo, which is the quickest one to include any changes.
http://www.bioconductor.org/packages/devel/bioc/html/Ringo.html
Best regards,
Joern

Morten Hansen wrote:
>
> I have a problem with the Ringo package.
>
> I am trying to read in the results from a 1.5Kb Human Promoter Array 
> (CHP0150-HP1). I get the following error shown in below in the 
> "Output" section.
>
> The target.txt, spottype.txt and sessionInfo() is shown below the 
> "Output" section.
>
> **************
> *** Output ***
> **************
> > myDir <- c("/home/mhansen/R/ChIP-chip/39037")
> > myRg <- readNimblegen("targets.txt","spottypes.txt", path = myDir)
> Reading targets file...
> Reading raw intensities...
> Read header information
> Read /home/mhansen/R/ChIP-chip/39037/39037_532_pair.txt
> Read /home/mhansen/R/ChIP-chip/39037/39037_635_pair.txt
> Error in RG$R[, i] <- obj[, columns$f] :
>   number of items to replace is not a multiple of replacement length
> >
>
>
>
> The target.txt and spottype.txt look like this:
> ******************
> *** target.txt ***
> ******************
> SlideNumber     FileNameCy3     FileNameCy5     Species Cy3     Cy5
> HSAP0406        39037_532_pair.txt      39037_635_pair.txt      Homo 
> sapiens (human)    total   HSAP0406
>
> ********************
> *** spottype.txt ***
> ********************
> SpotType        GENE_EXPR_OPTION        PROBE_ID        Color
> Probe   BLOCK1  *       black
>
>
> ********************
> *** sessionInfo()***
> ********************
> > sessionInfo()
> R version 2.6.2 (2008-02-08)
> x86_64-unknown-linux-gnu
>
> locale:
> ...
>
> attached base packages:
> [1] tools     stats     graphics  grDevices utils     datasets
> methods   base
>
> other attached packages:
>  [1] Ringo_1.2.0          RColorBrewer_1.0-2   vsn_3.2.1 
> affy_1.16.0          preprocessCore_1.0.0 affyio_1.6.1         
> limma_2.12.0
>  [8] geneplotter_1.16.0   lattice_0.17-8       annotate_1.16.1 
> xtable_1.5-2         AnnotationDbi_1.0.6  RSQLite_0.6-8
> DBI_0.2-4         [15] Biobase_1.16.3
>
> loaded via a namespace (and not attached):
> [1] grid_2.6.2         KernSmooth_2.22-22 rcompgen_0.1-17
> >