[BioC] problem read.maimage("Agilent") -limma

[Gordon K Smyth]

> Date: Mon, 25 Jul 2005 12:22:22 -0400
> From: Naomi Altman <naomi at stat.psu.edu>
> Subject: [BioC] problem read.maimage("Agilent") -limma
> To: bioconductor at stat.math.ethz.ch
>
> I am having trouble reading the Agilent arabidopsis 22575 gene array using
> read.maimage in Limma under R 2.1.1 (I don't know the limma version, but I
> just downloaded using the R packages interface, and also used the update,
> so I presume this is the most recent.

You should have limma 2.0.2.

> Under R 2.0.1, there was no problem reading all the data in the arrays using:
>
> RGf=read.maimages(c("2792.txt","2793.txt","2796.txt","4507.txt","4508.txt","4509.txt"),source="agilent"
> )
>
> dim(RGf$R)
> 22575     6
>
>
> But under R 2.1.I,  I get:
>
> RGf=read.maimages(c("2792.txt","2793.txt","2796.txt","4507.txt","4508.txt","4509.txt"),source="agilent"
> )
>
> dim(RGf$R)
> 12956    6
>
> The last line of RGf$R is all NA.
>
> The problem might be in RGf$genes.  When I try to print any row up to the
> last one, everything looks normal.  Trying to print the last row kills
> R.  The annotation for this gene appears to be exceptionally long.

I've just tried reading in some AgilentFE data and didn't have any problems.  So I wasn't able to
reproduce the error that you describe.

Try isolating which input file is causing the problem.  If you don't find a solution, you could
zip up an example data file which causes the error and send it to me.

Gordon


> Naomi S. Altman                                814-865-3791 (voice)
> Associate Professor
> Bioinformatics Consulting Center
> Dept. of Statistics                              814-863-7114 (fax)
> Penn State University                         814-865-1348 (Statistics)
> University Park, PA 16802-2111