Question

difficulty of using getSYMBOL with lumi nuID

0

Entering edit mode

Zhang,Jiexin ▴ 20

@zhangjiexin-3367

Last seen 9.2 years ago

United States

Dear all, I've been having difficulty extracting gene symbol using nuID. I've tried human and mouse, neither of them works. For example: > nuID # a nuID from mouse data [1] "WVEy90fXI4J7yrxXpk" > getSYMBOL(nuID,'lumiMouseAll.db') Error in lookUp(x, data, "SYMBOL") : SYMBOL is an invalid element name Would anyone give me some suggestions how to get gene symbol for Illumina data? Thanks a lot! Jiexin *********************************************************** To do great work, you have to have a pure mind. Everything else is human weakness. -- Mikhail Gromov *********************************************************** [[alternative HTML version deleted]]

• 1.0k views

ADD COMMENT • link updated 15.7 years ago by Sean Davis 21k • written 15.7 years ago by Zhang,Jiexin ▴ 20

score 0 · Answer 1 · 2009-03-26

0

Entering edit mode

Sean Davis 21k

@sean-davis-490

Last seen 3 months ago

United States

On Thu, Mar 26, 2009 at 5:52 PM, Zhang,Jiexin <jiexinzhang@mdanderson.org>wrote: > Dear all, > > I've been having difficulty extracting gene symbol using nuID. I've tried > human and mouse, neither of them works. For example: > > nuID # a nuID from mouse data > [1] "WVEy90fXI4J7yrxXpk" > > getSYMBOL(nuID,'lumiMouseAll.db') > Error in lookUp(x, data, "SYMBOL") : SYMBOL is an invalid element name > > Would anyone give me some suggestions how to get gene symbol for Illumina > data? Thanks a lot! > > get('WVEy90fXI4J7yrxXpk',lumiMouseAllSYMBOL) [1] "Slc38a5" > sessionInfo() R version 2.9.0 Under development (unstable) (2008-10-13 r46706) i386-apple-darwin9.0.0 locale: C attached base packages: [1] tools stats graphics grDevices utils datasets methods [8] base other attached packages: [1] lumiMouseAll.db_1.4.0 AnnotationDbi_1.3.12 RSQLite_0.7-0 [4] DBI_0.2-4 Biobase_2.1.7 [[alternative HTML version deleted]]

ADD COMMENT • link 15.7 years ago Sean Davis 21k

0

Entering edit mode

Thanks a lot for your help! Jiexin *********************************************************** To do great work, you have to have a pure mind. Everything else is human weakness. -- Mikhail Gromov *********************************************************** From: Sean Davis [mailto:seandavi@gmail.com] Sent: Thursday, March 26, 2009 4:59 PM To: Zhang,Jiexin Cc: bioconductor@stat.math.ethz.ch Subject: Re: [BioC] difficulty of using getSYMBOL with lumi nuID On Thu, Mar 26, 2009 at 5:52 PM, Zhang,Jiexin <jiexinzhang@mdanderson.org<mailto:jiexinzhang@mdanderson.org>> wrote: Dear all, I've been having difficulty extracting gene symbol using nuID. I've tried human and mouse, neither of them works. For example: > nuID # a nuID from mouse data [1] "WVEy90fXI4J7yrxXpk" > getSYMBOL(nuID,'lumiMouseAll.db') Error in lookUp(x, data, "SYMBOL") : SYMBOL is an invalid element name Would anyone give me some suggestions how to get gene symbol for Illumina data? Thanks a lot! > get('WVEy90fXI4J7yrxXpk',lumiMouseAllSYMBOL) [1] "Slc38a5" > sessionInfo() R version 2.9.0 Under development (unstable) (2008-10-13 r46706) i386-apple-darwin9.0.0 locale: C attached base packages: [1] tools stats graphics grDevices utils datasets methods [8] base other attached packages: [1] lumiMouseAll.db_1.4.0 AnnotationDbi_1.3.12 RSQLite_0.7-0 [4] DBI_0.2-4 Biobase_2.1.7 [[alternative HTML version deleted]]

ADD REPLY • link 15.7 years ago Zhang,Jiexin ▴ 20