[BioC] Help on Loading AgilentData into LIMMA

[Gordon Smyth]

Dear Nataliya,

David Pritchard (U Washington) has written off-line and has diagnosed the 
problem. The Agilent 44K arrays contain a single double-quote character on 
the last line that limma reads, which converts the rest of the file into a 
gene description.

The solution is to tell limma not to look for quote characters in your 
file, that is you should use

RG <- read.maimages(files=targets$fileName, path=loadPath, 
source="agilent", quote="")

Hopefully this will work for you
Gordon

 > Date: Tue, 08 Nov 2005 00:45:45 +0100
 > From: Nataliya Yeremenko <eremenko at science.uva.nl>
 > Subject: [BioC] Help on Loading AgilentData into LIMMA
 > To: BioC Mailing List <bioconductor at stat.math.ethz.ch>
 >
 > I'm coming back to my problem of import of Agilent data into the
 > Bioconductor
 > limma package.
 > Version of R is 2.2.0
 > Limma as well is the newest possible as I've installed Bioconductor only
 > two weeks ago.
 >
 > Each "target" file is Agilent 44K Human oligo microarray,
 > produced by FeatureExtraction 7.5.
 > I'm importing data into limma with:
 >  > RG <- read.maimages(files = targets$fileName, path = loadPath, source
 > = "agilent")
 > Afterwards checking the dimensions of RG with dim(RG) - 6195 rows only,
 > with no difference how many target files I've been loading.
 >
 > I go further and checked the same function on another data set -
 > Agilent custom 11K oligo microarrays extracted as well with Feature
 > Extraction 7.5
 > (with the same default settings of Feature extraction procedure as for 44K).
 > And to my surprise the target files have been loaded completely into LIMMA.
 > Dim(RG) -  8635 rows.
 >
 > So the problem is that of 44K - maybe target files are to big?
 >
 > Does anybody have any suggestions?
 >
 > --
 > Dr. Nataliya Yeremenko
 >
 > Universiteit van Amsterdam
 > Faculty of Science
 > IBED/AMB (Aquatische Microbiologie)
 > Nieuwe Achtergracht 127
 > NL-1018WS Amsterdam
 > the Netherlands
 >
 > tel. + 31 20 5257089
 > fax  + 31 20 5257064