Hey I have an odd problem:
I was using the oligo package to do RMA on some affy miRNA microarray data. It seems that the oligo package combines mutiple probes into one expression value automatically during the normalization process. Thats been great.
Now I would like to do cyclic loess normalization on the same data, but the function I have been using to do this normalizeBetweenArrays()
C_loessNorm_cyclicLoess <- normalizeBetweenArrays(C_miRNA_wholechip_2rem_for_Loess.mat,method=NULL, targets=NULL, cyclic.method="fast" )
Does not perform the same summation step. I looked into some other functions that required setting up a special package "mirna40cdf" but after following some other posts' instructions on doing that, any attempt to normalize using this package crashed R.
Is there a stand-alone function that can just summarize/combine the probes without doing a normalization step so that I can just feed that particular function the results of my cyclic loess via the normalizebetweenarrays() function?
