I have a question about the use of the frma function.
I have to put several datasets from GEO series together in a same big analysis. However, for each of these datasets (that is each specific GSE serie) I have to select only some specific patients (selection of specific GSM samples).
I downloaded the .cel files for all of the selected GSM samples.
Now, I want to normalize all these samples and I'm asking myself about the best solution between the following ones:
- Read all my .cel files whatever the dataset (that is whatever the GSE identifier) into a same Affybatch object and apply frma on this object
- For each GSE serie, first apply frma on all .cel files and then select the normalized patients I need to analyze
- For each GSE serie, first select the .cel for the patients I need to analyze and then apply frma only for these patients. I'm wondering if the 2 last solutions are equivalent.
I hope I'm clear enough. Thank you for your help.