[BioC] DNA micro-array normalization

[Thomas Hampton]

If all your samples share the same median, that is likely due to  
normalization, not luck. So you
could just plot or summarize your sets to get a reasonable answer to  
your question.

There are lots of ways to normalize, however, and it behooves the  
analyst to know what has been
done to the data before you write up the results. Saying, "the data  
were probably normalized"
isn't going to sound too persuasive in a paper.

I suggest you ask the people who gave you that data this question  
rather than engaging in some sort of forensic
quest...

Best,

Tom




On Feb 16, 2010, at 2:47 PM, avehna wrote:

> 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
>
> 	[[alternative HTML version deleted]]
>
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