How to use cdf version20 with oligo package
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sylvia ▴ 10
@sylvia-5630
Last seen 6.3 years ago

HI

Sorry if this is obvious, but I was wondering how do people use custom cdf with oligo package ?

I downloaded the cdf version 20 from column 'O' for the hugene20 st array (pd.hugene20st.hs.entrezg_20.0.0.tar.gz) and installed the package and I tried to do something like this:

dat <- read.celfiles(filenames = list.celfiles(), pkgname = "pd.hugene20st.hs.entrezg")

and when I do:
> class(dat)
[1] "GenericFeatureSet"
attr(,"package")
[1] "oligoClasses"

The class of dat is GenericFeatureSet instead of  GeneFeatureSet which can not be use by rma pre-processing later on. Do people convert the GenericFeatureSet to GeneFeatureSet? or am I missing any steps when using the cdf file?

Thanks!

oligo cdf • 1.7k views
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@james-w-macdonald-5106
Last seen 4 hours ago
United States

Why do you think that GenericFeatureSet cannot be used by rma?

> showMethods(rma)
Function: rma (package oligo)
object="ExonFeatureSet"
object="ExpressionFeatureSet"
object="GeneFeatureSet"
object="GenericFeatureSet"
object="HTAFeatureSet"
object="SnpCnvFeatureSet"

> sessionInfo()
R version 3.2.2 (2015-08-14)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 8 x64 (build 9200)

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] oligo_1.34.2        Biostrings_2.38.3   XVector_0.10.0     
[4] IRanges_2.4.6       S4Vectors_0.8.7     Biobase_2.30.0     
[7] oligoClasses_1.32.0 BiocGenerics_0.16.1

loaded via a namespace (and not attached):
 [1] affxparser_1.42.0          splines_3.2.2             
 [3] GenomicRanges_1.22.3       zlibbioc_1.16.0           
 [5] bit_1.1-12                 foreach_1.4.3             
 [7] GenomeInfoDb_1.6.2         tools_3.2.2               
 [9] SummarizedExperiment_1.0.2 ff_2.2-13                 
[11] DBI_0.3.1                  iterators_1.0.8           
[13] preprocessCore_1.32.0      affyio_1.40.0             
[15] codetools_0.2-14           RSQLite_1.0.0             
[17] compiler_3.2.2             BiocInstaller_1.20.1   
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Hi James,

I might have load affy package at the same time and didn't specify which rma to use and when I read the arguments for rma from oligo package the object is : Exon/HTA/Expression/Gene/SnpCnv-FeatureSet so I thought it doesn't take GenericFeatureSet! Sorry for the confusion, now it works!

Thanks!

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