I just want to have a clarification: is gExpress at the end of the aroma ST 
vignette* in log2 scale or not? Where in the analysis would we add the 
command to make the data log scale if it is not already in log scale? (or 
should we simply log2 the matrix output?).

Also, is it necessary to log2 transform the gExprs data in order to 
correctly perform an unpaired t test? I recently did a t test on some 
Aroma-normalized ST array data which resulted in a lot of p values of "1" 
when the p values were adjusted with Benjamini Hochberg, and now I'm 
wondering if it could possibly be that I did not log transform the data 
before conducting the t test.

Pardon if these are simple questions, but I'm new to the ST array 
normalization process.
~ Heather


On Wednesday, November 30, 2011 9:38:49 PM UTC-5, xiaowei guan wrote:
> Hello Henrik,
> May I ask you a question about using the 
> http://www.aroma-project.org/node/38 Vignette to derive the gene centric 
> values for HuGene-1_0-st-v1 array? I follow the command, but it only 
> generated the probe level data.... Is there a way to derive the gene symbol 
> not the probe level data?  
> Another question is that is the binary cdf file in the website from hg18?
> My probe names are as follows... the dimension is 31,252* the number of my 
> samples.
>  7892501  7892502  7892503  7892504 I am wondering do I need to download 
> the Netaffy probe annotation csv file to derive the data set with only gene 
> symbol? Could you please provide me with some guidance?
> Thanks very much in advance!
> best,
> Xiaowei

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