I want to extract up-regulated and down regulated genes in Myotonic dystrophy type 1 (DM1) from microarray dataset available at NCBI GEO database (http://www.ncbi.nlm.nih.gov/geo/). I downloaded the datasets from NCBI GEO in “GEO2R’’ format. Kindly, tell me about analysis through R or which method would be easier?
GEO2R is not a format but a tool. If the dataset is Chip-based, the normalized expression file will be there to download on the bottom of the GEO dataset page, which is taken as input during analysis by the Geo2R tool in that database. So, you can simply perform a GEO2R after making two groups from the available samples in that tool only and determine DEG by it. Otherwise, just download the entire normalized expression file and use it in R.
Have a look at this. You might not need any other thing.
https://www.ncbi.nlm.nih.gov/geo/info/geo2r.html
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