Question: problem with package version of rat2302 1.8.5
0
gravatar for Kimpel, Mark W
14.0 years ago by
Kimpel, Mark W890 wrote:
I have installed the newest version of annotation package rat2302, ver 1.8.5 . I have encountered what appears to be a discrepancy between the external and internal package version information. The code that reproduces this is below. Am I looking at this wrong or is this an issue that can be addressed? Mark Mark W. Kimpel, M.D. > sessionInfo() R version 2.2.0, 2005-08-29, i386-pc-mingw32 attached base packages: [1] "tools" "methods" "stats" "graphics" "grDevices" "utils" [7] "datasets" "base" other attached packages: affy reposTools Biobase rat2302 "1.7.2" "1.6.2" "1.7.0" "1.8.5" > getPkgVers("rat2302") [[1]] [1] "1.8.4"
ADD COMMENTlink modified 14.0 years ago by Seth Falcon7.4k • written 14.0 years ago by Kimpel, Mark W890
Answer: problem with package version of rat2302 1.8.5
0
gravatar for Ting-Yuan Liu FHCRC
14.0 years ago by
Ting-Yuan Liu FHCRC780 wrote:
Hi Mark, The function "getPkgVers" will read the version information from a file called "liblisting.Rda" in your library paths. The function "sessionInfo" will find out which packages are loaded and then read the version information from their DESCRIPTION files directly. I think the information in your liblisting.Rda file is not up-to-dated (for some reason) so that the results from these two functions are different. HTH, Ting-Yuan On Tue, 27 Sep 2005, Kimpel, Mark William wrote: > I have installed the newest version of annotation package rat2302, ver > 1.8.5 . > I have encountered what appears to be a discrepancy between the external > and internal package version information. The code that reproduces this > is below. > > Am I looking at this wrong or is this an issue that can be addressed? > > Mark > > Mark W. Kimpel, M.D. > > > > sessionInfo() > R version 2.2.0, 2005-08-29, i386-pc-mingw32 > > attached base packages: > [1] "tools" "methods" "stats" "graphics" "grDevices" "utils" > > [7] "datasets" "base" > > other attached packages: > affy reposTools Biobase rat2302 > "1.7.2" "1.6.2" "1.7.0" "1.8.5" > > > getPkgVers("rat2302") > [[1]] > [1] "1.8.4" > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >
ADD COMMENTlink written 14.0 years ago by Ting-Yuan Liu FHCRC780
Answer: problem with package version of rat2302 1.8.5
0
gravatar for Seth Falcon
14.0 years ago by
Seth Falcon7.4k
Seth Falcon7.4k wrote:
On 28 Sep 2005, tliu at fhcrc.org wrote: > > Hi Mark, > > The function "getPkgVers" will read the version information from a > file called "liblisting.Rda" in your library paths. The function > "sessionInfo" will find out which packages are loaded and then read > the version information from their DESCRIPTION files directly. > > I think the information in your liblisting.Rda file is not > up-to-dated (for some reason) so that the results from these two > functions are different. Right, geetPkgVers is from reposTools. There is a function syncLocalLibList that will update the liblisting.Rda file Ting mentioned. At this point, I recommend using sessionInfo() to determine what version of a package you actually have installed. Thanks for the report. + seth
ADD COMMENTlink written 14.0 years ago by Seth Falcon7.4k
Hello: I am a fist time trying to analyze cdna data and right at the first step i was bombed. can any one please help me: >library(Biobase) >library(marray) >samples = read.phenoData("phenodata.txt",header=TRUE, as.is = TRUE) > files = samples$fileName spree of errors starts here: ## the .XLS files are downloaded from Garber_lung data. ## software used in GenePix ## path : I am using windows based R so changed the ## directory to where all my .XLS files area locatd > mdata = read.GenePix(files, path=".") Error in if (skip > 0) readLines(file, skip) : missing value where TRUE/FALSE needed >mdata = read.GenePix(files, ext = 'xls') Error in if (skip > 0) readLines(file, skip) : missing value where TRUE/FALSE needed > mdata = read.marrayRaw(files,ext = "xls") Error in if is.na(pattern)) { : argument is of length zero > nmdata = read.marrayRaw(nfs, ext="xls") Error in if is.na(pattern)) { : argument is of length zero > nmdata = read.marrayRaw(nfs, ext="xls", skip = 22) Reading ... ./shu058.248-97_LCLC.xls Error in read.table(f, skip = skip2, header = TRUE, sep = sep, quote = quote, : unused argument(s) (ext ...) How do I read these XLS files and retain all the inforamtion. can any one please give R commands till I get to normalization procedure. Thank you srini
ADD REPLYlink written 14.0 years ago by Srinivas Iyyer590
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 338 users visited in the last hour