Search
Question: Oligo package RMA() function giving error
0
gravatar for Jo
2.3 years ago by
Jo10
Jo10 wrote:

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.

ADD COMMENTlink modified 2.3 years ago by Benilton Carvalho4.2k • written 2.3 years ago by Jo10
1
gravatar for Benilton Carvalho
2.3 years ago by
Brazil/Campinas/UNICAMP
Benilton Carvalho4.2k wrote:

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 COMMENTlink modified 2.3 years ago • written 2.3 years ago by Benilton Carvalho4.2k

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 REPLYlink modified 2.3 years ago • written 2.3 years ago by Jo10
1

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 REPLYlink written 2.3 years ago by Benilton Carvalho4.2k

It worked! Thank You.

ADD REPLYlink written 2.3 years ago by Jo10

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 REPLYlink written 2.3 years ago by James W. MacDonald45k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 278 users visited in the last hour