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

[k. brand]

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