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Question: How to analyse clariom d human files
1
gravatar for yusuf.khan
5 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. 

ADD COMMENTlink modified 5 months ago • written 5 months ago by yusuf.khan10
0
gravatar for James W. MacDonald
5 months ago by
United States
James W. MacDonald44k 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)
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.

ADD COMMENTlink written 5 months ago by James W. MacDonald44k
0
gravatar for yusuf.khan
5 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 ?

 

 

ADD COMMENTlink written 5 months ago by yusuf.khan10

Yes, that's fine. It's just telling you that some of the probesets map to multiple things. By default you only get one of the multiple mapped IDs. You can for example get all of the multiple mapped IDs, but in practice is easier to just go with the defaults.

ADD REPLYlink written 5 months ago by James W. MacDonald44k
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