I am trying to normalize a dataset GSE45220 based on hugene.1.1.st.v1 platform. However, when i try to do rma or gcrma normalization, i get an error about the missing cdf-file which does not work for the package anyway.
#GSE45220 BiocManager::install("GEOquery") library(GEOquery) library(dplyr) BiocManager::install("gcrma") library(gcrma) BiocManager::install("pd.hugene.1.1.st.v1") library(pd.hugene.1.1.st.v1) BiocManager::install("hugene10sttranscriptcluster.db") library(hugene10sttranscriptcluster.db) untar("GSE45220_RAW.tar", exdir="data1") cels = list.files("data1/", pattern = "CEL") sapply(paste("data1", cels, sep="/"), gunzip) cels = list.files("data1/", pattern = "CEL") raw.data=ReadAffy(filenames=cels)
The affy package can process data from the Gene ST 1.x series of arrays, but you should consider using either the oligo or xps packages, which are specifically designed for these arrays.
Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘rma’ for signature ‘"AffyBatch"’
I then tried oligo package but the problem persisted. SCAN also did not work, giving me this error Error in as.character.default(x) : no method for coercing this S4 class to a vector
Has anyone been through the same experience? I can use the processed data but normalizing myself would be much better i think.
I am using R version 3.6.0.