Question

normalization

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xpzhang ▴ 90

@xpzhang-780

Last seen 10.2 years ago

Hi, everyone! I am a graducate student in Institute of Genetic and Developmental Biology, Chinese Academy of Sciences. I have some data of microarray to be analysised.My microarray experiment only related Cy3. I prepared different probes with Cy3 by reverse transcription,and these probes were from one control and 5 treatment.Then there was 1 hybridization reaction in each slide. Then I will normalize these data. I want use R and Bioconductor to do it. I downloaded R 1.9.0 for windows and installed it,then installed Bioconductor package. Now, I have a question. Could be output the normalized data? 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. Could anyone help me? Thank you very much! XiaopengZHANG<xpzhang@genetics.ac.cn>

Transcription Microarray Transcription Microarray • 944 views

ADD COMMENT • link updated 20.5 years ago by Jean Yee Hwa Yang ▴ 920 • written 20.5 years ago by xpzhang ▴ 90

score 0 · Answer 1 · 2004-05-28

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Jean Yee Hwa Yang ▴ 920

@jean-yee-hwa-yang-104

Last seen 10.2 years ago

> 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

ADD COMMENT • link 20.5 years ago Jean Yee Hwa Yang ▴ 920

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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) 1 2 3 4 5 ... 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 difficult. Thank you very much! On Fri, 28 May 2004 11:52:03 -0700 (PDT) Jean Yee Hwa Yang <jean@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@genetics.ac.cn>

ADD REPLY • link 20.5 years ago xpzhang ▴ 90