[BioC] RMA/QuantileNormalization results difference between oligo and aroma.affymetrix for Hugene

[Mikhail Pachkov]

On Fri, Feb 26, 2010 at 5:48 PM, Benilton Carvalho
<beniltoncarvalho at gmail.com> wrote:
> Dear Mikhail,
>
> when you read the CEL files, you have the information at the probe
> level. So, when you summarize, you will summarize to a 'less granular'
> level (in this case probeset).
>
> Maybe what you're trying to achieve is the comparison of the
> background correction (or possibly normalization) method *before*
> summarization?

You are right we need expression data on *probe-level* without summarization.

Comparison is not my goal. I am just trying to learn how to use these
packages and choose one for our project. The discrepancy between
results was very confusing so I asked for help. Obviously the reason
was my ignorance.

In our project we need to read cel files and get expression values (bg
corrected and normalized) on *probe-level* for further analysis.

Best regards,

Mikhail