Normalization of non-normalized .txt data from GEO
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.
Thanks
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Googling will easily get you what you need, for example start with the following workflows:
Analysing Microarray Data In Bioconductor
http://bioinformatics.knowledgeblog.org/2011/06/20/analysing-microarray-data-in-bioconductor/
https://www.bioconductor.org/help/workflows/arrays/
http://wiki.bits.vib.be/index.php/Analyze_GEO_data_with_GEO2R
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.