ERROR in loading data through rma

Question

[muhammadzubair777]

i am facing problem in loading data through rma in R. when i have run the command

rmaData = rma(gse28403preset)

it is giving following error!

Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘rma’ for signature ‘"AffyBatch"’

code is here:

celFiles<- unlist(list.files("GSE28403",pattern="\\.CEL.gz",full.names=TRUE))

gse28403preset=ReadAffy(filenames=celFiles)

rmaData = rma(gse28403preset)

Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘rma’ for signature ‘"AffyBatch"’

can anyone give me any suggestion to solve this problem?

Answer 1

[Ar]

You error suggests that apart from affy R package there is another package in your workspace where rma function is defined. The command objects in these packages are also different. Therefore, R can't identify which rma function you are trying to use leading to this error. Another package where rma function is defined is oligo Try using:

> rma.data <- affy::rma(gse28403preset)

You should get:

Background correcting
Normalizing
Calculating Expression