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List:       bioconductor
Subject:    [BioC] Exonmap & xmapcore covdesc variable problem
From:       "Prime, John" <primej () MedImmune ! com>
Date:       2012-06-29 18:46:21
Message-ID: 2D4DB57D287AD14DA261524E57B48BF136E71A97 () GBCB1EMP001 ! medimmune ! com
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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@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
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