[BioC] using simpleaffy incorrectly, or is there a problem with the read.affy function?

[k. brand]

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