[BioC] Post rma analysis

Rafael A. Irizarry ririzarr at jhsph.edu
Wed Aug 20 01:35:21 MEST 2003

they are already logged. rma doesnt subtract mm and uses a conservative
background correction procedure so your minimum resulting expression
values are usually around 8. thus the minimum log2 is around 3. if i were
to do a t-test i would use the log scale expression values that rma gives

On Wed, 20 Aug 2003, Adaikalavan Ramasamy wrote:

> Dear all,
> I have performed rma() on several CEL files. Here is the summary of this
> expression data :
>     Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
>    2.674   5.021   6.150   6.144   7.151  14.420 
> The mean and variance of all arrays/columns are very close. A boxplot
> shows that the arrays are on comparable scales.
> However, these values are all positive. Do we take the log2
> transformation followed by column median centering or use these rma
> output ? I am worried that this might make a difference if we use t-test
> or any other parametric tests.
> Can anyone help me ? Many thanks.
> Regards, Adai
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