how can I use Lumi package for GSE31699 file?

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9.7 years ago

SCA ▴ 10

I would like to use lumi package for normalize to http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE31699

I read csv file and get a matrix file. I tried to use the steps in http://www.bioconductor.org/packages/release/bioc/vignettes/lumi/inst/doc/lumi.pdf but it doesn't work.

My questions:

How can I normalize to the my matrix file?
What should I do for using this package?

Thanks in advance

R • 3.3k views

ADD COMMENT • link updated 2.5 years ago by Ram 44k • written 9.7 years ago by SCA ▴ 10

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Is there supposed to be a question here?

Edit: Ah, there's a question now, great!

ADD REPLY • link 9.7 years ago by Devon Ryan 104k

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Why do you want to normalize the matrix file ? Its already normalized -

"The data was preprocessed by Bioconductor lumi package (version 2.5.5). It was vst transformed and quantile normalized."

ADD REPLY • link 9.7 years ago by poisonAlien ★ 3.2k

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Thank you very much for your information. I am very new about bioinformatics and R so these knowledge is very helpful for me.

I look at there its useful for expression data analysis and I check my matrix and your saying data is not same. it is for just 1 sample but I have 36 samples. I have raw data matrix both methylation data and expression data so I have to normalized. actually doesn't matter be which packet lumi or others. I just want to normalized these matrix and than according to distribution (normal- non normal) I will use parametric tests. I will be most grateful, if you could help me.

ADD REPLY • link updated 2.5 years ago by Ram 44k • written 9.7 years ago by SCA ▴ 10

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