Dear everyone
I am a newbie user of R Bioconductor. But I tried to follow some tutorials fromthe internet and I still can not found the solution for this error
I am trying to do an analysis using GSE52817 as a dataset
and this is what I have done:
R version 3.2.2 (2015-08-14) -- "Fire Safety"
Copyright (C) 2015 The R Foundation for Statistical Computing
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'citation()' on how to cite R or R packages in publications.
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'help.start()' for an HTML browser interface to help.
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> #settingworkdirectory
> setwd("C:/Users/mochammad/Documents/coba010/GSE52817_RAW/")
Error in setwd("C:/Users/mochammad/Documents/coba010/GSE52817_RAW/") :
cannot change working directory
> setwd("C:/Users/mochammad/Documents/coba010/GSE52817_RAW/")
> # load the script from the internet that is used in install bioconductor
> source("http://bioconductor.org/biocLite.R")
Bioconductor version 3.2 (BiocInstaller 1.20.1), ?biocLite for help
> biocLite("oligo")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.2 (BiocInstaller 1.20.1), R 3.2.2 (2015-08-14).
Installing package(s) ‘oligo’
trying URL 'https://bioconductor.org/packages/3.2/bioc/bin/windows/contrib/3.2/oligo_1.34.0.zip'
Content type 'application/zip' length 57493555 bytes (54.8 MB)
downloaded 54.8 MB
package ‘oligo’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\mochammad\AppData\Local\Temp\Rtmpkl8GZy\downloaded_packages
Old packages: 'ensembldb', 'GenomicFeatures'
Update all/some/none? [a/s/n]: a
trying URL 'https://bioconductor.org/packages/3.2/bioc/bin/windows/contrib/3.2/ensembldb_1.2.1.zip'
Content type 'application/zip' length 1801139 bytes (1.7 MB)
downloaded 1.7 MB
trying URL 'https://bioconductor.org/packages/3.2/bioc/bin/windows/contrib/3.2/GenomicFeatures_1.22.6.zip'
Content type 'application/zip' length 2329611 bytes (2.2 MB)
downloaded 2.2 MB
package ‘ensembldb’ successfully unpacked and MD5 sums checked
package ‘GenomicFeatures’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\mochammad\AppData\Local\Temp\Rtmpkl8GZy\downloaded_packages
> biocLite("limma")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.2 (BiocInstaller 1.20.1), R 3.2.2 (2015-08-14).
Installing package(s) ‘limma’
trying URL 'https://bioconductor.org/packages/3.2/bioc/bin/windows/contrib/3.2/limma_3.26.3.zip'
Content type 'application/zip' length 4150683 bytes (4.0 MB)
downloaded 4.0 MB
package ‘limma’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\mochammad\AppData\Local\Temp\Rtmpkl8GZy\downloaded_packages
> # load the oligo library
> library(oligo)
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:parallel’:
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply,
parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from ‘package:stats’:
IQR, mad, xtabs
The following objects are masked from ‘package:base’:
anyDuplicated, append, as.data.frame, as.vector, cbind, colnames, do.call, duplicated, eval, evalq,
Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply, lengths, Map, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unlist, unsplit
Loading required package: oligoClasses
Welcome to oligoClasses version 1.32.0
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: Biostrings
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: IRanges
Loading required package: XVector
====================================================================================================================
Welcome to oligo version 1.34.0
====================================================================================================================
> # Read in the CEL files in the directory
> celFiles <- list.celfiles()
> affyRaw <- read.celfiles(celFiles)
All the CEL files must be of the same type.
Error: checkChipTypes(filenames, verbose, "affymetrix", TRUE) is not TRUE
> library(pd.hugene.1.0.st.v1)
Loading required package: RSQLite
Loading required package: DBI
> eset <- rma(affyRaw)
Error in rma(affyRaw) :
error in evaluating the argument 'object' in selecting a method for function 'rma': Error: object 'affyRaw' not found
So, what should I do to make it run properly?
Thank you very much
best regards,
Ichsan
