Question: Normalization of the Illumina HumanMethylation450 BeadChip data, platform GPL13534
2
gravatar for milady81
2.5 years ago by
milady8160
milady8160 wrote:

Hi all,

I want to normalize the Illumina Infinium methylation microarray data by lima, or by minfi or other programs you would recommend.

The online available GEO... has: *family.soft data, matrix file, and RAW data like: v1.1.bpm, v1.2.bpm, *.csv, manifest/header_descripton.xls. and RAW data with: TargetID Proband393_mother.Signal_A Proband393_mother.Signal_B Proband393_mother.Detection Pval Proband393_father.Signal_A Proband393_father.Signal_B Proband393_father.Detection Pval and so on....

I checked the lumi tutorial and the package required IDAT data.

Could anyone tell me what data should I use to the normalization? I want to get the Methylation fractions (of Beta value) and the genomic locations of them.

I would be very grateful for help. I am new in epigenetics and still learning.

Dorota

R genome • 1.2k views
ADD COMMENTlink modified 2.5 years ago • written 2.5 years ago by milady8160

Kevin, you are the best!!!! Thank you thank you thank you!!!!

If I need more help can I type to you?

Thank you again, very much Dorota

ADD REPLYlink written 2.5 years ago by milady8160
1

Sure, contact me any time!

ADD REPLYlink written 2.5 years ago by Kevin Blighe71k

If an answer was helpful you should upvote it, if the answer resolved your question you should mark it as accepted.
Upvote|Bookmark|Accept

ADD REPLYlink written 2.5 years ago by WouterDeCoster45k
6
gravatar for Kevin Blighe
2.5 years ago by
Kevin Blighe71k
Republic of Ireland
Kevin Blighe71k wrote:

Dear Dorota,

The normalised values for your project of interest, GSE89353, can be obtained by running this code:

library(Biobase)
library(GEOquery)

gset <- getGEO("GSE89353", GSEMatrix =TRUE, getGPL=FALSE)
if (length(gset) > 1) idx <- grep("GPL13534", attr(gset, "names")) else idx <- 1
gset <- gset[[idx]]

boxplot(exprs(gset)[,1:50])

j

--------------------------------------

You can then do further tests with this data using standard R functions, e.g., difference in mean between different groups, or use other packages like:

Kevin

ADD COMMENTlink modified 2.5 years ago • written 2.5 years ago by Kevin Blighe71k
1

Hi Kevin. I also noticed this problem. Can I just consider the fetched gset object(or series_matrix) as preprocessed/normalized expression value(beta value)?

ADD REPLYlink written 2.5 years ago by Chong Tang100
1

In this case, the data is almost certainly normalised, as judged by the boxplot. With the above code, I obtain the Series Matrix File, which is more than likely the normalised data for whatever GEO dataset you want. However, GEO state that they cannot guarantee that every Series Matrix File is normalised. So, one has to check each time.

ADD REPLYlink written 2.5 years ago by Kevin Blighe71k
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