[BioC] Help on Loading AgilentData into LIMMA

[Sean Davis]

[BioC] Help on Loading AgilentData into LIMMANataliya,

This is not due to the size of the file, but to special characters in the 
file itself causing premature end-of-file.  Gordon replied, if I recall, 
that this was a bug in R 2.1.0 and has been fixed in R 2.2.0.  Perhaps you 
could send version and sessionInfo, just to be sure what versions of 
everything you are using?  Also, you might want to look in the archive for 
Gordon's specific answer.

Sean

----- Original Message ----- 
From: Nataliya Yeremenko
To: BioC Mailing List
Sent: Monday, November 07, 2005 6:45 PM
Subject: [BioC] Help on Loading AgilentData into LIMMA


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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