I am trying to install and load the oneChannelGUI package to analyse .CEL file microarray data but keep running into an error.
I used:
source("http://bioconductor.org/biocLite.R")
biocLite(c("Biobase", "limma", "affylmGUI", "tkWidgets", "GOstats", "AnnotationDbi", "preprocessCore", "IRanges", "baySeq", "Rsamtools", "R.utils", "annotate", "genefilter", "maSigPro", "pamr", "pdmclass", "ChIPpeakAnno", "chipseq", "BSgenome", "Rgraphviz", "affy" ,"annaffy", "affyPLM", "multtest", "ssize", "sizepower", "siggenes", "RankProd", "org.Hs.eg.db", "org.Mm.eg.db", "org.Rn.eg.db", "edgeR", "metaArray", "MergeMaid", "biomaRt", "GenomeGraphs","AffyCompatible", "Biostrings", "rtracklayer", "Genominator", "hugene10sttranscriptcluster.db", "mogene10sttranscriptcluster.db", "ragene10sttranscriptcluster.db", "HuExExonProbesetLocation", "MoExExonProbesetLocation", "RaExExonProbesetLocation", "snow", "RmiR", "RmiR.Hs.miRNA", "R.utils", "EDASeq","DESeq", "DEXSeq","goseq", "BSgenome.Hsapiens.UCSC.hg19", "TxDb.Hsapiens.UCSC.hg19.knownGene", "oneChannelGUI","chimera", "cummeRbund"))
to install the package and it returns this error:
Error in data.frame(binary= binvers, source = srcvers, row.names = bins, : duplicate row.names: R.utils
So I try to load the package with ... library(oneChannelGUI) and this returns the following error
Loading required package: chimera
Loading required package: org.Hs.eg.db
Error : .onLoad failed in loadNameSpace() for 'org.Hs.eg.db', details:
call: match.arg(synchronous, c("off", "normal", "full"))
error: 'arg' must be NULL or a character vector
In addition: Warning messages:
1: package 'oneChannelGUI' was built under R version 3.0.3
2: package 'chimera' was built under R version 3.0.3
Error: package 'org.Hs.eg.db' could not be loaded
I have tried uninstalling and reinstalling all the packages, I have also tried the biocValid() function to see if some of the packages were too new, to convert them to the older versions, but nothing has worked. I can load the affylmGUI software but the error occurs when I try to load oneChannelGUI.
If anyone can help with this that would be great, thanks
