Dear all,

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.

Caroline

Sorry for the slow response (I'm on vacation at the moment). If you're using the default frma, then Levi is correct that all 3 options are identical. If you set summarize="random_effect" then all 3 options would produce different results. For most situations, the default version of frma works well. I would additionally suggest that you consider using the barcode function (also in the frma package) to convert your data to binary (expressed / unexpressed) calls or z-scores. This is one way to reduce some of the batch effects that likely exist between the GSEs you're combining.