Can't load Bioconductor package genomewidesnp6cdf in R

Question

[andbeonetraveler]

New to R and Bioconductor, and I'm working off of code I got from someone else. I do:

source("http://bioconductor.org/biocLite.R")

if (!requireNamespace("BiocManager", quietly = TRUE))
  install.packages("BiocManager")
BiocManager::install("affy", version = "3.8")
BiocManager::install("oligo", version = "3.8")
BiocManager::install("pd.genomewidesnp.6", version = "3.8")

library(Biobase)
library(affy)
library(oligo)
library(pd.genomewidesnp.6)

data <- ReadAffy('myfile.CEL')

'myfile.CEL' is a 69 MB .CEL file from a particular project in Synapse. You can see what data looks like after loaded into my environment on my stackoverflow question.

Then if I do eset <- rma(data) I get the error:

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

And if I do eset <- affy::rma(data) I get:

Error in getCdfInfo(object) : 
  Could not obtain CDF environment, problems encountered:
Specified environment does not contain GenomeWideSNP_6
Library - package genomewidesnp6cdf not installed
Bioconductor - genomewidesnp6cdf not available

Google searches are not telling me what genomewidesnp6cdf is, whether it's the same as pd.genomewidesnp.6, and why I don't have it. Anyone know?

Answer 1

[Santosh Anand]

library(oligo) has another rma(), which masks the rma() from library(affy). You may get the affy rma by using affy::rma(data)

[andbeonetraveler]

Please see above; if I do that I get:

Error in getCdfInfo(object) : 
  Could not obtain CDF environment, problems encountered:
Specified environment does not contain GenomeWideSNP_6
Library - package genomewidesnp6cdf not installed
Bioconductor - genomewidesnp6cdf not available

[Santosh Anand]

rma() is used for ExpressionData. What you have here is a SNP data. Instead you should use http://bioconductor.org/packages/release/bioc/html/crlmm.html

[andbeonetraveler]

It actually is expression data. (Unless the wrong file was uploaded to synapse or something.) I don't understand why it has this annotation as snp data. Is that the problem?

[Santosh Anand]

Indeed, it is a problem. Affy will automatically try to load the corresponding CDF file. See section 3 https://www.bioconductor.org/packages/devel/bioc/vignettes/affy/inst/doc/affy.pdf