[BioC] hugene10stv1probe?

[James W. MacDonald]

Hi Dan,

The probe sequence files for the Gene microarrays are slightly different 
from the previous generation 3' biased arrays, so this will require some 
modification of the matchprobes package to accommodate the differences.

Making the changes is actually trivial - the makeProbePackage() function 
will use an arbitrary function (called via the 'importfun' argument) to 
read in the data from a probe_tab file. If one wanted a probe package 
that is exactly the same as what we currently supply, you could modify 
the existing function readProbeDataAffy() to read in the extra columns 
in the file and then just discard them.

The question then remains; is this a good idea or not? I'm not sure it 
is, and I think we need to think about these new chips a bit to decide 
what the probe package should contain.

For instance, the sequences that they report are the reverse complement 
of the target sequences. I'm not sure what the sequences for the 3' 
biased arrays were, but we might want to make what is in the package 
consistent (or maybe not - new chip == new package?).

In addition, there are no MM probes on these chips. Instead there are 
just a bunch of control probes:

The usual AFFX probes
A chip control
Antigenomic background probes
Genomic background probes
Exonic normalization control probes
Intronic normalization control probes
Unmapped probes

Since there are no MM probes, these packages clearly won't be useful for 
gcrma(), so what are the use cases for the package? This is what will 
inform any further discussion.

So what were you planning to do with the package?

Best,

Jim



Dan Swan wrote:
> Hi everyone,
> 
> I've just been sent some data to analyse using the new(ish) Affymetrix
> Human Gene ST1.0 microarrays.
> 
> I notice a CDF package has been built:
> 
> https://stat.ethz.ch/pipermail/bioconductor/2007-June/017740.html
> 
> (with some caveats from Jim)
> 
> Are there probe sequence data files anywhere for this chip (or in
> development?).  If not any pointers as to how I might assemble one?
> I'm not used to receiving array data for arrays not listed here!
> 
> http://www.bioconductor.org/packages/release/AnnotationData.html
> 
> thanks,
> 
> Dan
> 

-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623