I am trying to code my own routines to calculate the RMA measure similar to RMA express or the affy Bioconductor package. I am having trouble getting my numbers to come out the same as the results from RMA Express.
I am currently working on the median polish step, so I am running RMA Express with NO background correction or quantile normalisation. When I run RMA Express with only one .CEL file, I would expect median polish to return the median for each probeset. This is not the case. i.e.
When I run RMA Express on a probeset with mean values (from the CEL file) 228 112 40 53 and standard deviations 31.3 15.1 5.2 8.5, RMA Express returns the result 77.045441 where I would expect RMA to return 82.5 (the median).
Could somebody tell me how RMA Express is getting this number?
*Edited to make things clearer.