Question: Microarray adata Normalization using GEO2R?
gravatar for mathavanbioinfo
4.0 years ago by
mathavanbioinfo50 wrote:

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

gene • 2.6k views
ADD COMMENTlink modified 3.9 years ago by yywang11310 • written 4.0 years ago by mathavanbioinfo50

If you want to remove non-informative feature,I suggest you using the GeneFilter package

There are some functions to eliminate non-informative features

ADD REPLYlink written 4.0 years ago by Shamim Sarhadi210
gravatar for yywang113
3.9 years ago by
United States
yywang11310 wrote:

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.

ADD COMMENTlink written 3.9 years ago by yywang11310
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