Exonmap & xmapcore covdesc variable problem
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Prime, John ▴ 10
Last seen 8.4 years ago
Dear All I'm fairly new to R & Bioconductor and am using Exonmap to analyse a large batch of affy exon arrays. All was working ok with the original covdesc file which just listed the location and file name of each .cel, but I needed to apply a more complex design table to the data so reran the script with the updated covdesc only to find it's having problems. Here's an example segment of the problem covdesc file:- expt.grp id cell.line tissue genetic.background phase tissue.of.origin sex Phase_IId/P815-S28.CEL P815_Sp P815-S28 P815 Spleen DBA_2J 2d Mast_cells Female Phase_IId/P815-S29.CEL P815_Sp P815-S29 P815 Spleen DBA_2J 2d Mast_cells Female Phase_IId/P815-S30.CEL P815_Sp P815-S30 P815 Spleen DBA_2J 2d Mast_cells Female my scripts is as follows:- Sys.setenv(R_XMAP_CONF_DIR="~/.exonmap") library(exonmap) xmapConnect("hssl") setwd( "/home/primej/Desktop/Syngeneic_Data") raw.data<-read.exon(covdesc="covdesc.txt") raw.data at cdfName<- "exon.pmcdf" tes <- rma(raw.data) The new covdesc.txt file doesn't create any errors when being read and the background correction, RMA normalisation and calculation of expression all work fine; but when I pData(tes) to access the pheno data the actual variable entries all contain <na>. str(tes) shows the same problem. see below for the pData output:- sample expt.grp id cell.line tissue genetic.background phase tissue.of.origin sex P815-S28.CEL 1 <na> <na> <na> <na> <na> <na> <na> <na> P815-S29.CEL 2 <na> <na> <na> <na> <na> <na> <na> <na> P815-S30.CEL 3 <na> <na> <na> <na> <na> <na> <na> <na> The fact that the covdesc file is read without any errors flagging and that the file names and column headers all read ok doesn't give me a clear idea why the variables aren't accepted while the others are. Are there length or character limits for variables in covdesc files? (I could no info on this). I got the same problem with xmapcore as well. Any ideas what is causing it to fail to read the variables? I'm hoping it's something obvious that can easily be fixed and most likely due to my inexperience. I've given the sessionInfo at the bottom. Many thanks for your help. John Prime ================================================================== sessionInfo() R version 2.12.1 (2010-12-16) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 [4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C [10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] exon.pmcdf_1.1 exonmap_2.8.0 RMySQL_0.8-0 DBI_0.2-5 RColorBrewer_1.0-5 [6] genefilter_1.32.0 affy_1.28.1 Biobase_2.10.0 loaded via a namespace (and not attached): [1] affyio_1.18.0 annotate_1.28.1 AnnotationDbi_1.12.1 preprocessCore_1.12.0 [5] RSQLite_0.9-4 splines_2.12.1 survival_2.36-2 tools_2.12.1 [9] xtable_1.5-6 To the extent this electronic communication or any of its attachments contain information that is not in the public domain, such information is considered by MedImmune to be confidential and proprietary. This communication is expected to be read and/or used only by the individual(s) for whom it is intended. If you have received this electronic communication in error, please reply to the sender advising of the error in transmission and delete the original message and any accompanying documents from your system immediately, without copying, reviewing or otherwise using them for any purpose. Thank you for your cooperation.
affy exonmap xmapcore affy exonmap xmapcore • 734 views

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