Dear list,

I'm running a microarray analysis from an Affymetrix MoGene 2.0 ST array set. The first obvious step in the analysis is to inspect the quality of the dataset using several metrics (boxplots, histograms, pseudo-images etc). Oligo package provides several utilities for this purpose.

I'm a little bit confused with pseudo-image plots from the whole set of data obtained through the image function from Oligo. Attached you'll find the image plot from one of the arrays and as you can see there is a lighter vertical band on the right hand side. This area seems different to the rest of array and it happens to each chip of the dataset.

I've also analyzed Affymetrix MoGene 1.0 ST array datasets and there were no lighter areas. I was wondering whether this is normal in 2.0 arrays (maybe, the probes in this area are not used) or it is indeed a problem.

Thanks in advance,

Javier

Image can be viewed here:

It's unused space on the array. These arrays are on a 1612 X 1612 grid:

> readCelHeader("2HR_1.CEL")
$filename
[1] "2HR_1.CEL"

$version
[1] 1

$cols
[1] 1612

$rows
[1] 1612

But not all columns are used:

> library(pd.mogene.2.0.st)
> con <- db(pd.mogene.2.0.st)
> z <- dbGetQuery(con, "select * from pmfeature;")
> range(z$x)
[1]    0 1498
> range(z$y)
[1]    0 1611