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Question: using simpleaffy incorrectly, or is there a problem with the read.affy function?
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gravatar for k. brand
10.9 years ago by
k. brand420
k. brand420 wrote:
Dear BioCers, After setting my working directory and loading simpleaffy, i fail to read in my .CEL files using: rawAandB <- read.affy() Error in file(file, "r") : unable to open connection In addition: Warning message: cannot open file './covdesc', reason 'No such file or directory' And using: rawAandB <- read.affy("covdesc.txt") Error in function (classes, fdef, mtable) : unable to find an inherited method for function "pData", for signature "phenoData" where my "covdesc.txt" file in the wd looks like this: region Tco1A.CEL one Tco2A.CEL one Tco3B.CEL one Tco4B.CEL one Tmi1A.CEL two Tmi2A.CEL two Tmi3B.CEL two Tmi4B.CEL two Tsh1A.CEL three Tsh2A.CEL three Tsh3B.CEL three Tsh4B.CEL three Session Info and other console details as below. Using "library(affy)" and "rawAandB <- ReadAffy()" i have no problems. So am i using simpleaffy incorrectly, or is there a problem with the read.affy function?? > library(simpleaffy) Loading required package: affy Loading required package: Biobase Loading required package: tools Welcome to Bioconductor Vignettes contain introductory material. To view, type 'openVignette()' or start with 'help(Biobase)'. For details on reading vignettes, see the openVignette help page. Loading required package: affyio Loading required package: genefilter Loading required package: survival Loading required package: splines Welcome to 'simpleaffy' V 2.4.0 Produced by The Paterson Institute for Cancer Research and funded by CANCER RESEARCH UK. http://bioinformatics.picr.man.ac.uk/simpleaffy mailto: microarray at picr.man.ac.uk > ?read.affy > rawAandB <- read.affy() Error in file(file, "r") : unable to open connection In addition: Warning message: cannot open file './covdesc', reason 'No such file or directory' > rawAandB <- read.affy("covdesc.txt") Error in function (classes, fdef, mtable) : unable to find an inherited method for function "pData", for signature "phenoData" > sessionInfo() R version 2.4.0 (2006-10-03) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] "splines" "tools" "methods" "stats" "graphics" "grDevices" [7] "utils" "datasets" "tcltk" "base" other attached packages: simpleaffy genefilter survival affy affyio Biobase svIO "2.4.2" "1.12.0" "2.30" "1.12.0" "1.2.0" "1.12.0" "0.9-5" R2HTML svMisc svSocket svIDE "1.58" "0.9-5" "0.9-5" "0.9-5" > -- Karl Brand <k.brand at="" erasmusmc.nl=""> Department of Genetics Erasmus MC Dr Molewaterplein 50 3015 GE Rotterdam lab +31 (0)10 408 7409 fax +31 (0)10 408 9468
ADD COMMENTlink modified 10.9 years ago • written 10.9 years ago by k. brand420
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gravatar for k. brand
10.9 years ago by
k. brand420
k. brand420 wrote:
Biocers, Updating to the latest simpleaffy- 2.8.0- solved the problem... thanks again, karl on 1/18/2007 7:25 PM k. brand said the following: > Dear BioCers, > > After setting my working directory and loading simpleaffy, i fail to > read in my .CEL files using: > > rawAandB <- read.affy() > > Error in file(file, "r") : unable to open connection > In addition: Warning message: > cannot open file './covdesc', reason 'No such file or directory' > > And using: > > rawAandB <- read.affy("covdesc.txt") > Error in function (classes, fdef, mtable) : > unable to find an inherited method for function "pData", for > signature "phenoData" > > where my "covdesc.txt" file in the wd looks like this: > > region > Tco1A.CEL one > Tco2A.CEL one > Tco3B.CEL one > Tco4B.CEL one > Tmi1A.CEL two > Tmi2A.CEL two > Tmi3B.CEL two > Tmi4B.CEL two > Tsh1A.CEL three > Tsh2A.CEL three > Tsh3B.CEL three > Tsh4B.CEL three > > Session Info and other console details as below. > > Using "library(affy)" and "rawAandB <- ReadAffy()" i have no problems. > > So am i using simpleaffy incorrectly, or is there a problem with the > read.affy function?? > > > > > library(simpleaffy) > Loading required package: affy > Loading required package: Biobase > Loading required package: tools > > Welcome to Bioconductor > > Vignettes contain introductory material. To view, type > 'openVignette()' or start with 'help(Biobase)'. For details > on reading vignettes, see the openVignette help page. > > Loading required package: affyio > Loading required package: genefilter > Loading required package: survival > Loading required package: splines > Welcome to 'simpleaffy' V 2.4.0 > Produced by The Paterson Institute for Cancer Research > and funded by CANCER RESEARCH UK. > http://bioinformatics.picr.man.ac.uk/simpleaffy > mailto: microarray at picr.man.ac.uk > > ?read.affy > > rawAandB <- read.affy() > Error in file(file, "r") : unable to open connection > In addition: Warning message: > cannot open file './covdesc', reason 'No such file or directory' > > rawAandB <- read.affy("covdesc.txt") > Error in function (classes, fdef, mtable) : > unable to find an inherited method for function "pData", for > signature "phenoData" > > > sessionInfo() > R version 2.4.0 (2006-10-03) > i386-pc-mingw32 > > locale: > LC_COLLATE=English_United States.1252;LC_CTYPE=English_United > States.1252;LC_MONETARY=English_United > States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 > > attached base packages: > [1] "splines" "tools" "methods" "stats" "graphics" > "grDevices" > [7] "utils" "datasets" "tcltk" "base" > > other attached packages: > simpleaffy genefilter survival affy affyio Biobase > svIO > "2.4.2" "1.12.0" "2.30" "1.12.0" "1.2.0" "1.12.0" > "0.9-5" > R2HTML svMisc svSocket svIDE > "1.58" "0.9-5" "0.9-5" "0.9-5" > > > -- Karl Brand <k.brand at="" erasmusmc.nl=""> Department of Genetics Erasmus MC Dr Molewaterplein 50 3015 GE Rotterdam lab +31 (0)10 408 7409 fax +31 (0)10 408 9468
ADD COMMENTlink written 10.9 years ago by k. brand420
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