[BioC] problem with reading agilent microarray data into agi4x44preprocess

Jarek Bryk bryk at evolbio.mpg.de
Mon May 18 18:13:38 CEST 2009


I am trying to read my Agilent single color whole mouse genome 
microarray data into Agi4x44PreProcess, as described in the vignette. 
However, I get the error:

Error in readGenericHeader(fullname, columns = columns, sep = sep) :
Specified column headings not found in file

Following the advice from Martin Morgan (using options(error=recover) 
etc., see 
https://stat.ethz.ch/pipermail/bioconductor/2007-October/019577.html) I 
figured out that the error is caused by the lack of the BGUsed column in 
my raw data text file. And I don't know how to fix it. Is there a way of 
telling the read.maimages/read.AgilentFE to skip this column (I can't 
find this solution in the read.maimages help), or to modify the raw data 
files so that the function doesn't complain (simply pasting the column 
header does not work, I tried...)?

 > sessionInfo()
R version 2.9.0 (2009-04-17)


attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] mgug4122a.db_2.2.11     RSQLite_0.7-1           DBI_0.2-4 
     Agi4x44PreProcess_1.4.0 genefilter_1.24.0       annotate_1.22.0 
      AnnotationDbi_1.6.0     limma_2.18.0
[9] Biobase_2.4.1

loaded via a namespace (and not attached):
[1] splines_2.9.0   survival_2.35-4 tools_2.9.0     xtable_1.5-5

I would be very grateful for help,

   Jarek Bryk
   Max Planck Institute for Evolutionary Biology
   August Thienemann Str. 2 | 24306 Plön, Germany
   tel. +49 4522 763 287 | bryk at evolbio.mpg.de

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