Question: Normalization of non-normalized .txt data from GEO
gravatar for garimav89
4.0 years ago by
garimav890 wrote:

I have downloaded a non-normalized .txt file from GEO and now want to do median and quantile normalization and background normalization of this data.

My .txt file looks like this:

ID_REF 1A 1B 2A 2B hsa-miR-199b-3p 328 1532 1136 288 hsa-miR-302c -88 -44 -104 -136 hsa-miR-499-5p -24 -40 -48 -104 hsa-miR-768-3p 1032 1841 1424 848

Can anyone share R-script to proceed with the normalization step? Your help is really appreciated.


microarray R • 1.6k views
ADD COMMENTlink written 4.0 years ago by garimav890

Googling will easily get you what you need, for example start with the following workflows:
Analysing Microarray Data In Bioconductor

ADD REPLYlink written 4.0 years ago by WouterDeCoster45k

I wonder if anyone had success using info from these URL to normalise non-normalized .txt file from GEO. I went through the URL to no avail. Please help you have and R-Script.

ADD REPLYlink written 3.8 years ago by Apexy0
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