I'm using FIRMA algorithm, and I would like to use an existing FIRMA model (for instance one trained on 50 arrays) on new data (e.g. 2 new arrays).
I am able to train a FIRMA model (and an RMA model) quite easily using the doFIRMA (and doRMA) functions, which work quite well. However, I am not sure how I could extract the existing models to calculate FIRMA scores for the new data. To be more specific, I understand that FIRMA has basically 5 steps: -RMA steps- 1) background correction 2) normalization 3) summarization -FIRMA steps- 4) calculate residuals from fitting the standard RMA model 5) calculate the FIRMA score. I know that I could copy all 52 arrays (i.e. the old and the new) into a single folder and rerun the RMA / FIRMA algorithms on all data. However, this will become slower (and probably less necessary) as I get more and more data. I understand based on the link below that Step 1 treats each array independently, and I imagine that I can use the models (steps 2-4) calculated from the 50 old experiments on the 2 new experiments. However, I don't know how to do that. * https://groups.google.com/forum/#!searchin/aroma-affymetrix/FIRMA$20same$20model$20on$20new$20data/aroma-affymetrix/Ime1c6DjzBs/7n-vTdo3pCgJ Can you please help? Thank you, -Sam -- -- When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/ --- You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group. To unsubscribe from this group and stop receiving emails from it, send an email to aroma-affymetrix+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/groups/opt_out.
