Question: how can I use Lumi package for GSE31699 file?
0
gravatar for SCA
5.1 years ago by
SCA0
Turkey
SCA0 wrote:

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 doesnt work.  

my questions:

1) How can I normalize to  the my matrix file?

2) What sould I do for using this package? 

 

thanks in advance 

R • 2.0k views
ADD COMMENTlink modified 5.1 years ago • written 5.1 years ago by SCA0
1

Is there supposed to be a question here?

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

ADD REPLYlink modified 5.1 years ago • written 5.1 years ago by Devon Ryan94k

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 REPLYlink written 5.1 years ago by poisonAlien2.8k

 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 doesnt matter be which packet lumi or others. I just wnat to normalized these matrix and than according to distribution (normal- non normal) I will use parametric tests. I will be most greatful, if you could help me, . 

ADD REPLYlink modified 5.1 years ago • written 5.1 years ago by SCA0
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