[R] readaff() problem

[Amit Sengupta]

 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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