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 > Any suggestions? Morten Hansen MD ICMM, Panum institute University of Copenhagen Email: mhansen at imbg.ku.dk

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 > >