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"
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
>
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
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
