Question: Normalization of non-normalized .txt data from GEO
0
gravatar for garimav89
2.9 years ago by
garimav890
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.

Thanks

microarray R • 1.1k views
ADD COMMENTlink written 2.9 years ago by garimav890

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

ADD REPLYlink written 2.9 years ago by WouterDeCoster42k

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 2.7 years ago by Apexy0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 682 users visited in the last hour