oligo rma() function giving unused argument error
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Jiayi Sun ▴ 40
@jiayi-sun-4938
Last seen 5.1 years ago

I am trying to process the Clariom S Human array through oligo and I'm encountering errors at the rma normalization step.  

# load relevant packages
library(oligo)

# read in affy files
exonCELs <- list.celfiles(paste0(rootdir, datadir), full.names = TRUE)
exonES <- read.celfiles(exonCELs)

I get the error using both probeset and transcript as an option, although only transcript applies in this array.

> exonPS <- rma(exonES, target = "probeset")
Error in .local(object, ...) : unused argument (target = "probeset")
> exonPS <- rma(exonES, target = "transcript")
Error in .local(object, ...) : unused argument (target = "transcript")

I have tried the function without the target argument but the number of transcripts seems to be different than the number on the array.  I have also compared the output between using expression console and R and the same probes have significantly different values.

Here is my exonES object:

ExpressionFeatureSet (storageMode: lockedEnvironment)
assayData: 300304 features, 16 samples 
  element names: exprs 
protocolData
  rowNames: WTPlus_Liver_Rep1_ClariomS_Hu.CEL
    WTPlus_Liver_Rep2_ClariomS_Hu.CEL ...
    WTPlus_Testes_Rep4_ClariumS_Hu.CEL (16 total)
  varLabels: exprs dates
  varMetadata: labelDescription channel
phenoData
  rowNames: WTPlus_Liver_Rep1_ClariomS_Hu.CEL
    WTPlus_Liver_Rep2_ClariomS_Hu.CEL ...
    WTPlus_Testes_Rep4_ClariumS_Hu.CEL (16 total)
  varLabels: index
  varMetadata: labelDescription channel
featureData: none
experimentData: use 'experimentData(object)'
Annotation: pd.clariom.s.human 

And my sessionInfo():

> sessionInfo()
R version 3.3.3 (2017-03-06)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

locale:
[1] LC_COLLATE=English_United States.1252 
[2] LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

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

other attached packages:
 [1] pd.clariom.s.human_3.14.1 pdInfoBuilder_1.38.0     
 [3] affxparser_1.46.0         data.table_1.10.4        
 [5] BiocInstaller_1.24.0      DBI_0.6-1                
 [7] RSQLite_1.1-2             oligo_1.38.0             
 [9] Biostrings_2.42.1         XVector_0.14.1           
[11] IRanges_2.8.2             S4Vectors_0.12.2         
[13] Biobase_2.34.0            oligoClasses_1.36.0      
[15] BiocGenerics_0.20.0      

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.10               splines_3.3.3             
 [3] GenomicRanges_1.26.4       zlibbioc_1.20.0           
 [5] bit_1.1-12                 lattice_0.20-34           
 [7] foreach_1.4.3              GenomeInfoDb_1.10.3       
 [9] tools_3.3.3                SummarizedExperiment_1.4.0
[11] grid_3.3.3                 ff_2.2-13                 
[13] iterators_1.0.8            digest_0.6.12             
[15] preprocessCore_1.36.0      affyio_1.44.0             
[17] Matrix_1.2-8               bitops_1.0-6              
[19] codetools_0.2-15           RCurl_1.95-4.8            
[21] memoise_1.0.0      

 

 

oligo rma • 931 views
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Entering edit mode
@james-w-macdonald-5106
Last seen 15 minutes ago
United States

There is no target argument for the Clariom S arrays:

> dat <- read.celfiles(fn)
Loading required package: pd.clariom.s.mouse
Loading required package: RSQLite
Loading required package: DBI
Platform design info loaded.
<snip>
> class(dat)
[1] "ExpressionFeatureSet"
attr(,"package")
[1] "oligoClasses"

and if we look at ?rma we see

  ## S4 method for signature 'ExpressionFeatureSet'
     rma(object, background=TRUE, normalize=TRUE, subset=NULL)

This is because there is only one way to summarize these arrays, so there is no need to give anybody a choice.

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