[R] scaling on normlized data set

[Ben Bolker]

hosnaw <hmnawaz <at> gmail.com> writes:

> I am using R and tried to normalize the data within each sample group using
> RMA. When I tried to import the all the normalized expression data as a
> single text file and make a boxplot, it showed discrepancy among the sample
> groups.  I tried to scale them or re-normalize them again, so that it can be
> used for further analysis. Unfortunately, I did not manage it on using
> AffyPLM package. Would you please help me out with this problem.

  I suggest you try your question on the Bioconductor mailing lists;
I suspect you'll have a better chance of an answer there. It would also
be helpful to provide a reproducible example, and more detail about
what 'I did not manage it' means.

  good luck
    Ben Bolker