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Question: How to analyse clariom d human files
1
14 months ago by
yusuf.khan10
yusuf.khan10 wrote:

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.

modified 14 months ago • written 14 months ago by yusuf.khan10
0
14 months ago by
United States
James W. MacDonald46k wrote:

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)
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.

0
14 months ago by
yusuf.khan10
yusuf.khan10 wrote:

> 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 ?