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How to Normalize the Microarray Data Obtained from ncbi?
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3.7 years ago
India

I have micro array data in GSE format from http://www.ncbi.nlm.nih.gov/geo/geo2r/?acc=GSE1739. My simple question is how to normalize this data ? All I could see was gene symbols and IDs. I could not find numbers to normalize (As my background is Mathematics, very poor knowledge about gene data). I know there is one R package limma with function normalizeWithinArrays. But no idea how to implement on the data set mentioned above. Please provide some insight. Thanks in advance.

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2.8 years ago
al3n70rn • 100
France

Have a look to GEOquery package.

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Dear al3n70rn, thanks for quick reply. I checked it but could not find any function for normalization of my data. I am also getting some errors in this package. I posted this error here: http://stackoverflow.com/questions/27687215/error-in-using-getgeo-command-of-geoquery-package-of-r-for-bioinfomatic and could not get any solution for this.

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17 months ago
National Institutes of Health, Bethesda…

The GEOquery package can access the data and pull them into R. Before using GEOquery, though, you'll have to decide on whether you are going to start with "raw" data which is often available via NCBI GEO or with the processed data. The processed data are generally already normalized (based on the submitter's workflow).

In general, though, there is not a single approach that works for all data from GEO. You'll need to go through the process of quality control, learning about the array platform being used, and the general approaches for normalization of that platform.

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Dear Sean Davis,

Thanks for your comment, for normalization I can see only numbers and can implement various techniques, but most confusing point for me is the link I posted above contains some gene symbols. I can not see numbers. Please help in this direction.

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GEO2R is for online investigation of data in GEO. You cannot alter the normalization already done there. If you want to normalize the data differently, you'll need to download the datasets yourself.

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5.2 years ago
Maastricht, The Netherlands

If I understand you correctly you look at this study: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE1739

For that study you can download the originally submitted data as "SOFT formatted family file(s)". That will normally contain raw data. Since this is Affymetrix that should include .cel files.

If you want to redo the QC and and normalisation on that I would personally use arrayanalysis.org (but that is because we created that). It will allow you to study the QC using reports that are harmonised across methods, do normalisation and some basic statistical modelling and pathway analysis. Limma is indeed one of the (many) packages used by the pipeline there.