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

[Mikhail Spivakov]

Jim, thanks very much for explaning!
Best wishes,
Mikhail

On 2/1/10, James W. MacDonald <jmacdon at med.umich.edu> wrote:
> 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]]
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives:
>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>
> --
> 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
> **********************************************************
> Electronic Mail is not secure, may not be read every day, and should not be
> used for urgent or sensitive issues
>
>

-- 
Sent from my mobile device