Microarray adata Normalization using GEO2R?

Question

[mathavanbioinfo]

Hi Can share your knowledge with me? What is the difference between normalization done by the NCBI GEO2R and other commercial tools? Which one is best? In my deferentially gene expression list contain more than 3000 genes , i set up the parameter of adjusted p value less than 0.05 and logFC value greater than 1.5. I want to reduce the gene list by the changing the parameter is possible? Is that same genes have different probe id and different expression value?- Affymetrix

[Shamim Sarhadi]

If you want to remove non-informative feature,I suggest you using the GeneFilter package https://www.bioconductor.org/packages/release/bioc/html/genefilter.html

There are some functions to eliminate non-informative features

Answer 1

[yywang113]

There is no normalization in GEO2R, we need other methods to do this. If you run GEO2R in your own computer, you can set parameters yourself.

http://wiki.bits.vib.be/index.php/Analyze_GEO_data_with_GEO2R