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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