Hi all, I have a list of data sets like this that I downloaded from GEO:
GDS1279 GDS1280 GDS1311 GDS156 GDS1647 GDS1803 GDS2019 GDS2082
I just want to know whether the expression values in these datasets have been transformed using RMA, some other algorithm or not transformed. In reality I have a lot of data sets, so I was wondering what's the best way to take an input list like the example above, and turn it into:
GDS1279: RMA GDS1280: MAS5 GDS1311: RMA GDS156: RMA GDS156: Not transformed GDS1647: RMA etc
Someone told me to look in the soft files, I can see for example, for GDS4858 there's "dataset_value_type=transformed count", but not specifically what software/algorithm (e.g. RMA, MAS5) was picked? If someone could show me specifically where in the file this information is? Or alternatively, if you could show me for an example a webpage where I could get the information, I'll do it manually? I know there's also some code you can use for GEO, but I'm not familiar with it, if someone could provide sample code to obtain this info from GEO I'd also appreciate it.
Thanks for your time