[BioC] Help on Loading AgilentData into LIMMA
Gordon Smyth
smyth at wehi.edu.au
Tue Nov 8 23:54:09 CET 2005
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
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