Unable to get the Platform Table using fData on eset object
1
0
Entering edit mode
@sailu-yellaboina-3686
Last seen 9.6 years ago
Hi I am unable to get the plotform table using fData on eset object downloaded from ArrayExpress. Here is the example R code. library(ArrayExpress) dataset.name="E-TABM-493" data=trygetAEdataset.name, type="processed")) cn=getcolproc(data) eset=procset(data, cn[2]) platform=fData(eset) The platform is not coming in table format. Thank You Sailu Yellaboina Visiting Fellow NIEHS, NIH [[alternative HTML version deleted]]
ArrayExpress ArrayExpress • 784 views
ADD COMMENT
0
Entering edit mode
@wolfgang-huber-3550
Last seen 3 months ago
EMBL European Molecular Biology Laborat…
Dear Sailu you need to provide the output of "sessionInfo()" as well as the error message you get, or what eaxctly in the result that you get you think is wrong. What do you mean by "coming in table format"? Neither "coming" nor "table format" are well-defined concepts in the R language. When I just ran your code chunk, I got: > str(platform) 'data.frame': 45101 obs. of 17 variables: $ Composite.Element.Name : Factor w/ 45101 levels "Affymetrix:CompositeSequence:Mouse430_2:1415670_at",..: 45038 45039 45040 45041 45042 45043 45044 45045 45046 45047 ... $ Comment.AECompositeName. : Factor w/ 45101 levels "1415670_at","1415671_at",..: 45038 45039 45040 45041 45042 45043 45044 45045 45046 45047 ... $ ....[11 more elements] .... which seems alright to me. I also got, > eset=procset(data, cn[2]) Read 49 items Warning message: In eval(expr, envir, enclos) : Cannot attach phenoData > sessionInfo() R version 2.12.0 Under development (unstable) (2010-05-10 r51966) x86_64-unknown-linux-gnu locale: [1] LC_CTYPE=C LC_NUMERIC=C LC_TIME=C [4] LC_COLLATE=C LC_MONETARY=C LC_MESSAGES=la_AU.utf8 [7] LC_PAPER=C LC_NAME=C LC_ADDRESS=C [10] LC_TELEPHONE=C LC_MEASUREMENT=C LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices datasets utils methods base other attached packages: [1] ArrayExpress_1.9.0 Biobase_2.9.0 fortunes_1.3-7 loaded via a namespace (and not attached): [1] XML_3.1-0 affy_1.27.1 affyio_1.17.0 [4] limma_3.5.3 preprocessCore_1.11.0 Best wishes Wolfgang On 10/05/10 22:25, Sailu Yellaboina wrote: > Hi > I am unable to get the plotform table using fData on eset object > downloaded from ArrayExpress. > > Here is the example R code. > > library(ArrayExpress) > dataset.name="E-TABM-493" > data=try(getAEdataset.name, type="processed")) > cn=getcolproc(data) > eset=procset(data, cn[2]) > platform=fData(eset) > > The platform is not coming in table format. > > Thank You > Sailu Yellaboina > Visiting Fellow > NIEHS, NIH > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber
ADD COMMENT

Login before adding your answer.

Traffic: 731 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6