Hi,

I am a newbie in R

I have clariom dataset 21 files, six condition one control each have three replicates ((6+1=7)*3=21)

I did run following command 

p <- new("AffyHTAPDInfoPkgSeed",
          clfFile = "Clariom_D_Human.r1.clf",
          pgfFile = "Clariom_D_Human.r1.pgf",
          coreMps = "Clariom_D_Human.r1.mps",
          transFile = "Clariom_D_Human.na36.hg38.transcript.csv",
          probeFile = "Clariom_D_Human.na36.hg38.probeset.csv",
          author = "me",
          email = "mymail",
          genomebuild="hg38",
          organism="Homo Sapiens",
          species="Homo Sapiens",
          version = "0.0.1")

makepdInfopackage(p,unlike=True)

There was no error, it run fine.

but what to do after that. unable to go forward. how to use this. 

You didn't need to do that at all. You just need to start R in the directory that contains your celfiles and do

library(oligo)
dat <- read.celfiles(list.celfiles())
eset <- rma(dat)

If you then want to add annotations (and who doesn't?), you could use my affycoretools package

library(affycoretools)
library(clariomdhumantranscriptcluster.db)
eset <- annotateEset(eset, clariomdhumantranscriptcluster.db)

And then go on to using limma to make comparions. You need to read the limma User's guide if you are not familiar with that package.

> eset <- annotateEset(eset, clariomdhumantranscriptcluster.db)
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns

is this right ?