[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
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
More information about the Bioconductor