[BioC] Read Agilent 244k chip and QC

[Marc Noguera]

Hi all,
I am trying to read and visualize data obtained from an agilent chip.

For this purpose I use limma package and the read.maimages function as
follows

fileRG.raw <- read.maimages("File",source="agilent")

FileRG gets read correctly. When I check the dimensions it shows to have
243494 probes which seem to be correctly annotated. I, then attach the
layout for the chip from the GAL file:

galinfo <- readGAL(fileGAL)
fileRG.raw$printer<-getLayout(galinfo)

and try to plot R/G according to this prnter layout:

imageplot(log2(fileRG.raw$R),fileRG.raw$printer,zlim=c(0,9),main="R-For.RAW")

However, I obtain the following error:

> Error in imageplot(log2(fileRG.raw$R), fileRG.raw$printer, zlim = c(0,  :
>   Number of image spots does not agree with layout dimensions
Which is due to the fact that the gal file has 912*267 dimension
corresponding to 243504 probes. Checking the expression raw information
I see that there are 10 probes that are tagged as "ignore", which
read.maimages ignores convenientl but, then, I can't visualize R and G
channels (or MA info when obtained) because of this inconsistency.
If I add, by hand, ten probes in the expression file, imageplot works
fine but this is not the right thing to do.

What is the convenient thing to do? Any suggestion?

Thank you in advance

Marc

-- 
-----------------------------------------------------
Marc Noguera i Julian, PhD
Genomics unit / Bioinformatics
Institut de Medicina Preventiva i Personalitzada
del Càncer (IMPPC)
B-10 Office
Carretera de Can Ruti
Camí de les Escoles s/n
08916 Badalona, Barcelona