Question

problem with GDS2eSet

0

Entering edit mode

Youngik Yang ▴ 10

@youngik-yang-2931

Last seen 11.4 years ago

Hi, I've got following error messages whenever I run GDS2eSet. > eset <- GDS2eSet(gds) File stored at: /tmp/Rtmpa4UdPv/GPL59.soft Error in validObject(.Object) : invalid class "AnnotatedDataFrame" object: AnnotatedDataFrame colnames of data differ from row.names of varMetadata The following lines were obtained by sessionInfo(). R version 2.7.0 (2008-04-22) i386-redhat-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US .UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_N AME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTI FICATION=C attached base packages: [1] tools stats graphics grDevices utils datasets methods [8] base other attached packages: [1] limma_2.9.17 GEOquery_2.2.1 RCurl_0.9-3 Biobase_1.12.2 loaded via a namespace (and not attached): [1] biclust_0.5 flexclust_0.99-0 grid_2.7.0 lattice_0.17-6 [5] MASS_7.2-41 modeltools_0.2-15 stats4_2.7.0 Any help will be greatly appreciated. Thank in advance. Youngik.

• 901 views

ADD COMMENT • link updated 17.5 years ago by Sean Davis 21k • written 17.5 years ago by Youngik Yang ▴ 10

score 0 · Answer 1 · 2008-07-21

On Mon, Jul 21, 2008 at 5:31 PM, Youngik Yang <yiyang at="" indiana.edu=""> wrote: > Hi, > I've got following error messages whenever I run GDS2eSet. > >> eset <- GDS2eSet(gds) > > File stored at: > /tmp/Rtmpa4UdPv/GPL59.soft > Error in validObject(.Object) : > invalid class "AnnotatedDataFrame" object: > AnnotatedDataFrame colnames of data differ from row.names of varMetadata > > The following lines were obtained by sessionInfo(). > > R version 2.7.0 (2008-04-22) > i386-redhat-linux-gnu > > locale: > LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_ US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC _NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDEN TIFICATION=C > > attached base packages: > [1] tools stats graphics grDevices utils datasets methods [8] > base > other attached packages: > [1] limma_2.9.17 GEOquery_2.2.1 RCurl_0.9-3 Biobase_1.12.2 > > loaded via a namespace (and not attached): > [1] biclust_0.5 flexclust_0.99-0 grid_2.7.0 lattice_0.17-6 > [5] MASS_7.2-41 modeltools_0.2-15 stats4_2.7.0 Hello, Youngik. You have some significant version mismatch between your R version and bioconductor packages. You should use biocLite() to install the packages and upgrade GEOquery, Biobase, and potentially many other packages. If you still have problems, feel free to write again. Sean