Entering edit mode
k. brand
▴
420
@k-brand-1874
Last seen 9.6 years ago
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
