problem with human gene 2.0 st

[cbat...@uottawa.ca]

Hi,
I was wondering if there is a way I can analyze human gene 2.0 st arrays
using your software. The error message is follows:

FATAL ERROR: ProbesetSummarizeEngine::loadPgfLayout() - unable to handle
clf file without order set to col_major.

Skipping DABG p-value calculation to resolve (Bad library files -> contact
Affymetrix support)

OPerating system: 32 bit
Version: 2.0.7

Best
Cory Batenchuk

[Nathan Salomonis]

Hi Cory,

AltAnalyze's current databases are dedicated to the version 1.0 builds. It
looks like Affymetrix changed the probeset identifiers in the latest arrays
such that they don't overlap with previous versions. This means that
AltAnalyze doesn't know what to do with those probesets yet.

You can however use AltAnalyze to get normalized probeset level expression
values and dabg p-values back for this array (not transcript-cluster-level).
Just analyze as an Affymetrix gene array and select the PDF
(HuGene-2_0-st.pgf) file supplied with your arrays (folder should also have
a clf and antigenomics.bgp file) when prompted. Before APT was crashing for
you but you should get normalized expression values out just fine (I just
did this). AltAnalyze will still crash with an error after normalization,
because it has no probeset reference for this chip with the attached error.

To use in AltAnalyze, after it crashes, you would need to translate the
probesets from version 2.0 IDs to 1.0. I'm not sure the best way to do this
unless Affymetrix supplies a translation. We will try to deal with this in
the future but it does mess with AltAnalyze's current database schema (Gene
Array is of one type, not different versions). This is on our to-do-list
though.

If you just want gene-level data out you can use Affymetrix Power Tools (see
their documentation) and get some limited splicing analyses with MiDAS (also
with APT).

Let me know what you end up doing.

Best,
Nathan