r - How do I background correct an Illumina eset without using lumiB? -
i'm doing work publicly available microarray data sets i've downloaded geo. i'm having trouble using lumi package process illumina beadarray data.
normally when using lumi package use lumir convert data lumibatch object, use lumib on background correct. lumir requires bead standard errors in order create lumibatch object, in absence creates expression set. of lumi's functions work on expression sets, not lumib. data sets i've downloaded have mean intensity values , in cases associated p-value. therefore can't turn data lumibatch object , can't background correct lumib.
i appreciate suggestions on how background correct expression sets. apologies if i've phrased unhelpfully or left out important information, i'm new both r , asking questions on forum this.
thanks,
emma
this how i've been using lumir , how use lumib if lumibatch object:
#import data , convert lumibatch/eset object gsexxx.lumi <- lumir("gsexxx_raw_data.txt",lib.mapping="lumihumanidmapping") #using lumib background correct lumibatch object gsexxx.bgcorrected <- lumib(gsexxx.lumi,method=c('bgadjust','forcepositive'))
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