[BioC] affyBatch: probes from intensity table not listed in the output of indexProbes()

[James W. MacDonald]

Hi Mikhail,

Mikhail Spivakov wrote:
> Hello everyone,
> 
> I'm reading affy data using ReadAffy and have just noticed that the total
> number of probes listed in the intensity table is about 10k larger than the
> number of probes associated with probesets - at least as returned by
> indexProbes (see example below). I'm wondering if this is how it is supposed
> to be - and if so, whether these "orphan" probes are used in any way by any
> standard analysis procedures?

The short answers are 'yes' and 'no'.

If you look closely at an image of an affy chip you can see that there 
are a bunch of probes around the perimeter that alternate from bright to 
dark. These are used for instrument alignment when the chip is scanned.

There are also some that are used to tile down the chip name as well as 
some in the center of the chip as well. You can see these by zooming in 
on the top left corner. Using the Dilution dataset in affydata:

library(affy)
library(affydata)
data(Dilution)
a <- exprs(Dilution[,1])
a <- as.matrix(rev(as.data.frame(matrix(a, 640, 640))))
image(1:100, 1:100, log(a[1:100, 541:640]), col = gray(c(0:64)/64))

Since these probes are only used for alignment, they are ignored by all 
further processing of the data.

Best,

Jim




> 
> esExpDesc <- read.AnnotatedDataFrame("experimentDescription.txt", esPath,
> header=TRUE, sep = "\t", stringsAsFactors = TRUE, row.names=1)
> esAffyExp <- ReadAffy(filenames = rownames(pData(esExpDesc)), phenoData =
> esExpDesc, celfile.path = esPath, verbose = TRUE)
> nrow(exprs(esAffyExp))
> #[1] 1004004
> length(unlist(indexProbes(esAffyExp, which="both")))
> #[1] 992936
> 
> Many thanks
> Mikhail
> 
> ==
> Mikhail Spivakov PhD
> European Bioinformatics Institute
> Hinxton
> UK
> 
> 	[[alternative HTML version deleted]]
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
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