Hi There,

I've got a DNA microarray dataset that looks like this:

*    Probe                 Signal          Detection
Detection_p-value                   Descriptions*
AFFX-BioB-5_at       181                P
0.00011                  "E. coli  GEN=bioB  DB_XREF=gb:J04423.1"
AFFX-BioB-M_at     227.3              P                 0.000044
   "E. coli  GEN=bioB  DB_XREF=gb:J04423.1"
AFFX-BioC-5_at     499.2               P
0.000052                "E. coli  GEN=bioC  DB_XREF=gb:J04423.1"

I have control and treatment with 3 replicas for each one of them.

But I'm not sure whether these data have been already normalized, and on the
other hand, this is not the typical affymetrix format...

Could you help me in this regard? What is the typical signal range for rough
affymetrix data? (these data range from 0 to 9000)

If the data have been already normalized, Can I calculate the mean (for
treatment and control) followed by the differential expression of genes
without taking into account the "Detection" column?

(I guess I will need to build my ExpressionSet from scratch)

Thanks a lot (I'm a newbie in bioconductor and micro-array analysis). I will
appreciate you help!

Avhena

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