On 5/23/06 5:16 AM, "[EMAIL PROTECTED]" <[EMAIL PROTECTED]> wrote:
> Hi all,
>
> OK I realise my last post to this list was a bit of a ramble so let me ask
> something simpler. Thanks to Sean by the way for reading all the way to the
> end
> of it and making some useful suggestions. Can anyone explain to me in the
> simplest possible terms how to construct a reporter table for Affymetrix
> GeneChip
> probes? I've looked at the user guide to see what information is required and
> it
> seems that most of it is spread across the Affymetrix library files for each
> chip
> which I have now downloaded from their website. Is there an easy way to
> extract
> this information or do I have to set about dissecting it from the various
> files
> manually? Is this even the right way to approach this problem?
Try here:
ftp://ftp.tigr.org/pub/data/tgi/Resourcerer/Human
for Resourcerer data built by TIGR using information from various public
databases and from information provided by affymetrix. There are MANY
public resources where you can get Affy information including UCSC genome
browser, NIH DAVID database, Ensembl, and several others.
As an aside, if you haven't used perl before, if microarray data
manipulation is going to be a significant part of your job, you should learn
it (or R or matlab or python--take your pick). Scripting is nearly
absolutely required for extracting data from various sources and putting it
in another form.
Sean
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