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

[Henrik Bengtsson]

On Fri, Feb 26, 2010 at 6:13 PM, Mikhail Pachkov <pachkov at gmail.com> wrote:
> 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.

FYI, if you do:

library("aroma.affymetrix");
cs <- AffymetrixCelSet$byName("mine", chipType="HuGene-1_0-st-v1");
bc <- RmaBackgroundCorrection(cs);
csBC <- process(bc,verbose=verbose);
qn <- QuantileNormalization(csBC, typesToUpdate="pm");
csN <- process(qn);

then ou will end up with a new set of CEL files that are background
corrected and quantile normalized according to the RMA pipeline.
These files are located in getPath(csN).  These CEL files are regular
CEL files meaning you can use them in whatever software understanding
CEL files.

/Henrik

>
> Best regards,
>
> Mikhail
>
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