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ERROR in loading data through rma

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?

r
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updated by zx8754 zx8754 • written by muhammadzubair777 • muhammadzubair777

1 answer

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
• 1 views • link
written by ATRX ATRX

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