Question: microarray analysis (affymetrix) software or tools
0
gravatar for alromisashamoon
5.8 years ago by
United Kingdom
alromisashamoon0 wrote:

I am asking for a tool or online software for micoarray analysis (affymetrix) doing the normalization and annotation,online or free trial. i am looking for the different gene expression . would any one help me and guide me please. 

affymetrix microarray • 5.6k views
ADD COMMENTlink modified 5.6 years ago by Chris Evelo10.0k • written 5.8 years ago by alromisashamoon0
1
gravatar for Devon Ryan
5.8 years ago by
Devon Ryan94k
Freiburg, Germany
Devon Ryan94k wrote:

As poisonAlien mentioned, a very common toolset would be R with the affy and limma packages. You can go from raw .cel files to statistics with that and also relatively easily annotate the results to your liking.

ADD COMMENTlink written 5.8 years ago by Devon Ryan94k
1
gravatar for Chris Evelo
5.8 years ago by
Chris Evelo10.0k
Maastricht, The Netherlands
Chris Evelo10.0k wrote:

You are probably looking for something like our arrayanalysis.org which was described here. It uses a.o. the affy and limma Bioconductor packages mentioned by others.

ADD COMMENTlink modified 7 weeks ago by RamRS25k • written 5.8 years ago by Chris Evelo10.0k
0
gravatar for poisonAlien
5.8 years ago by
poisonAlien2.8k
Asgard
poisonAlien2.8k wrote:

Not sure about such tools (except some CLC paid stuff) or online sw.

But, if you are comfortable with R, there is this great tutorial on how to analyze Affymetrix data. Starting from reading .cel files to getting DEGs and clustering, heatmap, etc. It's fairly simple even if you are new to R.

If your data is from GEO, you can use GEO2R

ADD COMMENTlink modified 7 weeks ago by RamRS25k • written 5.8 years ago by poisonAlien2.8k
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