Hi,I am having a problem with the ReadAffy() in the university R programming
environment. I install affyPLM and invoke library(affyPLM) in the following
way. I have the cel files in the craig subdirectory. Please let me know how to
resolve the problem.Amit
source("http://bioconductor.org/biocLite.R";) biocLite("affyPLM")
biocLite("gcrma") library(affyPLM)>
setwd("c:/Users/amit.sengupta/Desktop/myRfolder/craig")
> craig.data=ReadAffy()
Error in AllButCelsForReadAffy(..., filenames = filenames, widget = widget, :
No cel filennames specified and no cel files in specified
directory:c:/Users/amit.sengupta/Desktop/myRfolder/craig
Included are the outputs of installations.
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preproc (5)
People Amit Sengupta Hi David, After installing bioclite, I invoke
library(affyplm) and run into this problem. > library(affyPLM) Loading required
package: affy Error: package ‘Biobase’ required by ‘affy’ could no Sep
29 at 12:43 PM Wheeler, David Linnard Hello Sir, I had similar
problems. For me I had to essentially resource bicolite everytime as below.
Also, try to put quotations around your package names after the bioclite
command, see it that works Sep 29 at 3:08 PM Hi David,This is the
problem now with ReadAffy(). I have all files in myRfolder. Let me know what
you think.Amit-------------------------------------------------------------
> source("http://bioconductor.org/biocLite.R";)
Bioconductor version 3.1 (BiocInstaller 1.18.4), ?biocLite for help
> biocLite("affyPLM")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.1 (BiocInstaller 1.18.4), R version 3.2.0.
Installing package(s) ‘affyPLM’
trying URL
'http://bioconductor.org/packages/3.1/bioc/bin/windows/contrib/3.2/affyPLM_1.44.0.zip'
Content type 'application/zip' length 5289800 bytes (5.0 MB)
downloaded 5.0 MB
package ‘affyPLM’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\amit.sengupta\AppData\Local\Temp\RtmpITiCKT\downloaded_packages
> biocLite("gcrma")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.1 (BiocInstaller 1.18.4), R version 3.2.0.
Installing package(s) ‘gcrma’
trying URL
'http://bioconductor.org/packages/3.1/bioc/bin/windows/contrib/3.2/gcrma_2.40.0.zip'
Content type 'application/zip' length 490279 bytes (478 KB)
downloaded 478 KB
package ‘gcrma’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\amit.sengupta\AppData\Local\Temp\RtmpITiCKT\downloaded_packages
> library(affyPLM)
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 object is masked from ‘package:stats’:
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, intersect,
is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax,
pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rep.int,
rownames, sapply, setdiff, sort, table, tapply, union, unique,
unlist, unsplit
Loading required package: affy
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: gcrma
Creating a generic function for ‘nchar’ from package ‘base’ in package
‘S4Vectors’
Loading required package: preprocessCore
Warning message:
package ‘affy’ was built under R version 3.2.1
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