Question

Oligo package RMA() function giving error

0

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Jo ▴ 30

@jo-8608

Last seen 8.3 years ago

Hello,

I am trying to pre process a dataset using the RMA function of the Oligo package:

library(oligo)

# Read in the CEL files in the directory
celFiles <- list.celfiles()
affyRaw <- read.celfiles(celFiles)

eset <- rma(affyRaw)

This code is giving me the error:

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

I am not sure what is wrong. Please advise on how it should be fixed.

oligo rma • 5.4k views

ADD COMMENT • link updated 8.7 years ago by Benilton Carvalho ★ 4.3k • written 8.7 years ago by Jo ▴ 30

score 1 · Answer 1 · 2015-08-13

1

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Benilton Carvalho ★ 4.3k

@benilton-carvalho-1375

Last seen 4.1 years ago

Brazil/Campinas/UNICAMP

Hi Jo,

can you please let me know the results of the command

sessionInfo()

right after you get the error, just so I can investigate the origin of the problem and propose a fix?

Many thanks, benilton

ADD COMMENT • link 8.7 years ago Benilton Carvalho ★ 4.3k

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Here it is. Thanks for your help!

R version 3.2.1 (2015-06-18)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.10.2 (Yosemite)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets methods base

other attached packages:
[1] BiocInstaller_1.18.4 pd.hugene.1.1.st.v1_3.14.1 RSQLite_1.0.0
[4] DBI_0.3.1 hgu133plus2cdf_2.16.0 affy_1.46.1
[7] oligo_1.32.0 Biostrings_2.36.1 XVector_0.8.0
[10] IRanges_2.2.5 S4Vectors_0.6.3 Biobase_2.28.0
[13] oligoClasses_1.30.0 BiocGenerics_0.14.0

loaded via a namespace (and not attached):
[1] AnnotationDbi_1.30.1 affxparser_1.40.0 GenomicRanges_1.20.5 splines_3.2.1
[5] zlibbioc_1.14.0 bit_1.1-12 foreach_1.4.2 GenomeInfoDb_1.4.1
[9] tools_3.2.1 ff_2.2-13 iterators_1.0.7 preprocessCore_1.30.0
[13] affyio_1.36.0 codetools_0.2-14

ADD REPLY • link 8.7 years ago Jo ▴ 30

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Entering edit mode

Can you please start a brand new R session and not load the affy package? Just start a new session and go with:

library(oligo)
celFiles = list.celfiles()
affyRaw <- read.celfiles(celFiles)
eset <- rma(affyRaw)

This issue can be issued by having the affy package loaded along with oligo.

ADD REPLY • link 8.7 years ago Benilton Carvalho ★ 4.3k

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It worked! Thank You.

ADD REPLY • link 8.7 years ago Jo ▴ 30

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Do note that it isn't a problem to have both packages loaded, but you just have to specify which version of rma() you want. You do this using the :: operator. To get the oligo version you just call oligo::rma(), and if you want the affy version you use affy::rma().

ADD REPLY • link 8.7 years ago James W. MacDonald 65k