[BioC] Help on Loading AgilentData into LIMMA

[Gordon K Smyth]

> 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.

Thanks for reporting the R version.  Your limma is not the newest possible however.  You
presumably have limma 2.2.0 whereas limma 2.3.3 is available on CRAN.  Please do upgrade limma
from CRAN as I suggested to you a couple of days ago.  Not only will you be trying out the current
software, but you'll find that limma will read your Agilent files many times faster.  See the
User's Guide Section 2.1 on the difference between installing from Bioconductor and CRAN.

> 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?

As Sean Davis has already mentioned, file size is very unlikely to be the problem.  There is no
size limit.  We had guessed before when you hadn't reported your R version that you might be
experiencing a known bug in R 2.1 which made it not possible to read Agilent files containing
backslash sequences.  However you're using R 2.2.0.

You seem to be experiencing a new problem we have not seen before.  If you email one of your 44K
input files to me directly (zip it up first) then we will trouble-shoot it.

Gordon

> 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