[BioC] is my normalization right?

xpzhang xpzhang at genetics.ac.cn
Sat May 29 09:21:55 CEST 2004

Thank you for your answer!

My raw-data was from GenePix. Because I used only Cy3 in my whole
microarray experiment, I only extract data by the software,and try to
normalize the data by Bioconductor. 

I made a .txt file for the raw data, it was just like this:

Gene Name  Contrl(intensity)   Treat1(intensity)   Treat2(intensity) Treat3(intensity) 

I want to use mutiple slides normalization with intensity dependent, is
it appropriate? And could you tell me howto? I am trying to find out
ways by reading Bioconductor's document and help files,but I feel really

Thank you very much!

On Fri, 28 May 2004 11:52:03 -0700 (PDT)
Jean Yee Hwa Yang <jean at biostat.ucsf.edu> wrote:

> > I have read the pdf files of marrayclasses, marrayinput, marraynorm, marrayplots and marraytools. And I have tested the command in marraynorm's chm help file. And I have not found out how to output the normalized data.
> Yes, you can output the files using
> A) 
> write.table(maM(swirl), file="test.txt", sep="\t")
> or
> B)
> In the new marray package, you can smiply output the file with
> library(marray)
> data(swirl)
> write.marray(swirl)
> Jean

Xiaopeng ZHANG<xpzhang at genetics.ac.cn>

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