I want to extract up-regulated and down regulated genes in crop plants from microarray dataset available at NCBI GEO database (http://www.ncbi.nlm.nih.gov/geo/). I downloaded dataset challenged by pathogen from NCBI GEO in “Series Matrix File’’ format. Kindly tell me about analysis through R.
Thanking you.
Hi
I don't know if I have understood ur problem right, but to my understanding in my opinion identifying up or down regulated genes isn't a problem at all if you have the right dataset. If u have the 'feature extracted' , ' log converted' values of the data then it should be easy. But of course you should have the data of gene expression of the reference sample. I assume u understand what the reference sample. Let us take for instance gene -X in the reference sample has an log expression value of 2 and in ur test the expression value for the gene is 5, then the gene in ur test is uprgulated , say the the expression value in the test is 0.5 then the gene is down regulated. That should be simple. The data set u have downloaded, identify the reference/ control and then work in identify the differentials regulated gene expression values in the test sample. I guess that was of help. U can mail me on the subject if u wish to.
rgds
prem
Hi,
you should also be able to use GEO2R if your experiment has a GEO accession number (http://www.ncbi.nlm.nih.gov/geo/geo2r/).
Put in the experiment number and you can get the top 250 differentially expressed genes, or a list of all, or the corresponding R scripts.
Thanks, Jana
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