[BioC] hugene10stv1probe?

[Dan Swan]

Jim et al,

> 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

Ahh.. this is all new information to me.. I probably should have read
the Affy site a little closer :/

> 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.

I think this is where I immediately fell down with my handling of
things - I assumed they were just a subset of the exon array or
related to the hgfocus arrays, but with a 'traditional' Affy setup -
obviously not.

I'll go back to the data and decide what I need before further comment..

Thanks!

Dan

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