Issue with [MOE430A] Affymetrix Mouse Expression 430A Array

Question

[shawin]

I have a data set which is for [MOE430A] Affymetrix Mouse Expression 430A Array

and i tried read the data and normaize it using the code bellow :

i download mouse430a2.db from the link bellow which is for bioconductor , https://www.bioconductor.org/packages/release/data/annotation/

but it does not work ?

   HCelfiles<-list.celfiles(full.names=TRUE)
   HCelfiles

   data<-read.celfiles(HCelfiles, pkgname="mouse430a2.db")

   HNorm<-rma(data)

  HNormData<-exprs(HNorm)

  write.csv(HNormData,"NormH.csv")

any suggestion kindly ?

Answer 1

[mastal511]

Make sure that the annotation package you use is the correct one for the array - the MOE430A and mouse430A2 are two different Affymetrix arrays.

What Bioconductor package are you using to analyse your data?

[shawin]

I have used pkgname="mouse430a2.db" for the chip which is :

[MOE430A] Affymetrix Mouse Expression 430A Array

and the oligo package is used for reading the cel files ??

[mastal511]

The oligo package is fine, you could also use the affy package.

You have to use the correct annotation package for the array. So if your data are from the Mouse 430A array, you need to get the bioconductor package for the 430A array. The 430A2 is a different array.

I think you don't actually have to use the package name parameter, by default the read.celfiles() function will automatically figure out, from the cel file, which package to use.