I tried to use below code to normalize my data before using combat to deal with batch effects:
- norm <- ReadAffy()
- norm.rma <-rma(norm)
Unluckily, my data include 3 data sets, 2 Affymetrix Human Genome U133 Plus 2.0 Array and 1 Affymetrix Human Gene 1.0 ST Array. I received this error message "Error in affyio::read_abatch(filenames, rm.mask, rm.outliers, rm.extra,: Cel file D:////batchdemo/GSMxxxx.CEL.gz does not seem to have the correct dimensions".
I tried to use dchip instead but again, I failed. I even couldn't input the data to dchip.
Any advice and suggestions will be greatly appreciated.