Hi Osee,
I think your email will get lost in the mix because you:
(a) replied to an ongoing thread with a new/different question. Please
just start a new thread by sending a fresh email to the group; and
(b) you're asking your question on the wrong group. Since you're
having problems with a bioconductor package, repost your question
there if you still can't figure out what's going on:
http://www.bioconductor.org/docs/mailList.html
-steve
On Mar 2, 2009, at 12:53 PM, Osee Sanogo wrote:
Hello,
I am a beginner in R and I am having the error message:
maqc <- read.xysfiles(xys.files)
Error in geometry(get(pkgname)) :
no slot of name "geometry" for this object of class "platformDesign"
Could someone tell me what this means and how to correct it?
Here is my session history with the error message at the end.
Thanks a lot
Osee
library(oligo)
Loading required package: Biobase
Loading required package: tools
Welcome to Bioconductor
Vignettes contain introductory material. To view, type
'openVignette()'. To cite Bioconductor, see
'citation("Biobase")' and for packages 'citation(pkgname)'.
Loading required package: splines
Loading required package: RSQLite
Loading required package: DBI
Loading required package: preprocessCore
Loading required package: AnnotationDbi
Loading required package: affxparser
Loading required package: oligoClasses
oligo Package - Series 1.5.x
Warning message:
package 'affxparser' was built under R version 2.8.1
library(maqcExpression4plex)
/-------------------------------------------\
| SAMPLE EXPRESSION DATA - MAQC/ HG18 - NGS |
|-------------------------------------------|
| Data provided by NimbleGen Systems (NGS). |
| This package is meant to be used only for |
| demonstration of BioConductor packages. |
|-------------------------------------------|
| The contents of this package are provided |
| in good faith and the maintainer does not |
| warrant their accuracy. |
\-------------------------------------------/
library(genefilter)
Loading required package: survival
library(geneplotter)
Loading required package: lattice
Loading required package: annotate
Loading required package: xtable
KernSmooth 2.22 installed
Copyright M. P. Wand 1997
library(limma)
library(RColorBrewer)
Warning message:
package 'RColorBrewer' was built under R version 2.8.1
palette(brewer.pal(8, "Dark2"))
library(splines)
library(RSQLite)
library(DBI)
library(preprocessCore)
library(AnnotationDbi)
library(affxparser)
library(oligoClasses)
library(survival)
library(lattice)
library(annotate)
library(xtablekkl)
Error in library(xtablekkl) : there is no package called 'xtablekkl'
library(xtable)
extdata <- system.file(".",
+ package="maqcExpression4plex")
xys.files <- list.xysfiles(".",
+ full.names=TRUE)
basename(xys.files)
[1] "15515902_532.xys" "15517302_532.xys" "15521702_532.xys"
"15524302_532.xys"
[5] "15524402_532.xys" "15524802_532.xys" "15524902_532.xys"
"15525102_532.xys"
[9] "15526302_532.xys" "15661702_532.xys"
maqc <- read.xysfiles(xys.files)
Loading required package: pd.2007.07.05.g.aculeatus.expr
Error in geometry(get(pkgname)) :
no slot of name "geometry" for this object of class "platformDesign"
library(pd.2007.07.05.g.aculeatus.expr)
maqc <- read.xysfiles(xys.files)
Error in geometry(get(pkgname)) :
no slot of name "geometry" for this object of class "platformDesign"
On 3/2/09 11:22 AM, "David Winsemius" <[email protected]> wrote:
In order to do that, the OP may need to open a Terminal window,
determine where the .Rhistory file resides, and issue the command
'rm .Rhistory'. The Mac GUI hides a lot of the system innards
including all the "." files.
_______________________________________________
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--
Steve Lianoglou
Graduate Student: Physiology, Biophysics and Systems Biology
Weill Medical College of Cornell University
http://cbio.mskcc.org/~lianos
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