Question

need help regarding microarray data analysis using limma

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varshika singh ▴ 20

@varshika-singh-5653

Last seen 10.3 years ago

Dear Sir/Madam I am using bioconductor package for analysis of Agilent two color data. After normalisation when i am giving command dat.m<-dat2$M, an error is shown as: Error in dat2$M : $ operator is invalid for atomic vectors. Kindly help what went wrong. [[alternative HTML version deleted]]

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ADD COMMENT • link updated 12.0 years ago by J.delasHeras@ed.ac.uk ★ 1.9k • written 12.0 years ago by varshika singh ▴ 20

score 0 · Answer 1 · 2012-12-13

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J.delasHeras@ed.ac.uk ★ 1.9k

@jdelasherasedacuk-1189

Last seen 9.4 years ago

United Kingdom

Quoting varshika singh <varshika13singh at="" gmail.com=""> on Thu, 13 Dec 2012 11:02:15 +0530: > Dear Sir/Madam > I am using bioconductor package for analysis of Agilent two color data. > After normalisation when i am giving command dat.m<-dat2$M, an error is > shown as: > Error in dat2$M : $ operator is invalid for atomic vectors. Kindly help > what went wrong. > > [[alternative HTML version deleted]] what is dat2? or, what do you get if you do: 'class(dat2)' Jose -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

ADD COMMENT • link 12.0 years ago J.delasHeras@ed.ac.uk ★ 1.9k

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And if it's not there, you can try to follow the instructions in this vignette from the AnnotationForge package to generate an appropriate chip package: www.bioconductor.org/packages/2.11/bioc/vignettes/AnnotationForge/inst /doc/SQLForge.pdf Marc On 12/13/2012 02:38 AM, J.delasHeras at ed.ac.uk wrote: > Quoting varshika singh <varshika13singh at="" gmail.com=""> on Thu, 13 Dec 2012 > 11:02:15 +0530: > >> Dear Sir/Madam >> I am using bioconductor package for analysis of Agilent two color data. >> After normalisation when i am giving command dat.m<-dat2$M, an error is >> shown as: >> Error in dat2$M : $ operator is invalid for atomic vectors. Kindly help >> what went wrong. >> >> [[alternative HTML version deleted]] > > > what is dat2? or, what do you get if you do: > > 'class(dat2)' > > Jose >

ADD REPLY • link 12.0 years ago Marc Carlson ★ 7.2k

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Oops. This went to the wrong thread. Please disregard... Marc On 12/13/2012 10:33 AM, Marc Carlson wrote: > And if it's not there, you can try to follow the instructions in this > vignette from the AnnotationForge package to generate an appropriate > chip package: > > www.bioconductor.org/packages/2.11/bioc/vignettes/AnnotationForge/in st/doc/SQLForge.pdf > > > > Marc > > > > On 12/13/2012 02:38 AM, J.delasHeras at ed.ac.uk wrote: >> Quoting varshika singh <varshika13singh at="" gmail.com=""> on Thu, 13 Dec >> 2012 11:02:15 +0530: >> >>> Dear Sir/Madam >>> I am using bioconductor package for analysis of Agilent two color data. >>> After normalisation when i am giving command dat.m<-dat2$M, an >>> error is >>> shown as: >>> Error in dat2$M : $ operator is invalid for atomic vectors. Kindly help >>> what went wrong. >>> >>> [[alternative HTML version deleted]] >> >> >> what is dat2? or, what do you get if you do: >> >> 'class(dat2)' >> >> Jose >> >

ADD REPLY • link 12.0 years ago Marc Carlson ★ 7.2k