rownames in topTable and posterior probability
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@adaikalavan-ramasamy-675
Last seen 9.6 years ago
topTable() in limma packages returns the row numbers and it would be useful to see the row names (i.e. Affy ID) instead. I am aware that I may supply the 'genelist' argument but help("topTable") says : genelist: data frame or character vector containing gene information. If not specified, this will be taken from the 'genes' component of 'fit'. My usual usage is as follows fit <- lmFit(onebatch, design) fit2 <- contrasts.fit( fit, cont.m ) fit2 <- eBayes(fit2) topTable(fit2) M t P.Value B 12358 -0.8636721 -7.585040 3.808592e-05 11.958486 48048 -0.8765769 -7.400093 7.417187e-05 11.363358 ... But I found no genes component in fit via fit$genes or str(fit). Same goes for fit2. I doing something wrong ? Thank you. Regards, Adai
affy limma affy limma • 1.5k views
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@gordon-smyth
Last seen 1 hour ago
WEHI, Melbourne, Australia
> Date: Fri, 25 Feb 2005 11:33:57 +0000 > From: Adaikalavan Ramasamy <ramasamy@cancer.org.uk> > Subject: [BioC] rownames in topTable and posterior probability > To: BioConductor mailing list <bioconductor@stat.math.ethz.ch> > > topTable() in limma packages returns the row numbers and it would be > useful to see the row names (i.e. Affy ID) instead. topTable() already does this, as can be seen from the case studies in the User's Guide. For example, the Ecoli and Estrogen case studies show top tables with Affy IDs included automatically. > I am aware that I > may supply the 'genelist' argument but help("topTable") says : > > genelist: data frame or character vector containing gene > information. If not specified, this will be taken > from the 'genes' component of 'fit'. This is not normally required. Have you not looked at the examples in the User's Guide? > My usual usage is as follows > > fit <- lmFit(onebatch, design) > fit2 <- contrasts.fit( fit, cont.m ) > fit2 <- eBayes(fit2) > > topTable(fit2) > M t P.Value B > 12358 -0.8636721 -7.585040 3.808592e-05 11.958486 > 48048 -0.8765769 -7.400093 7.417187e-05 11.363358 > ... > > But I found no genes component in fit via fit$genes or str(fit). Same > goes for fit2. I doing something wrong ? You haven't told use what sort of object 'onebatch' is. If onebatch is an object from which gene names can be extracted, e.g., an exprSet, then they should be included in 'fit'. If 'onebatch' doesn't include gene names, you can't really expect them to be in fit. Gordon > Thank you. > > Regards, Adai
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Hi, Where can I get Hu6800 annotation files and the probe target sequences. I cannot find these at NetAffx site. Is there any way, I can get target sequences as FASTA formatted files? Thanks S. Peri
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S Peri wrote: > Hi, > Where can I get Hu6800 annotation files and the probe > target sequences. I cannot find these at NetAffx site. The Hu6800 is also known as the HuGeneFl chip. http://www.affymetrix.com/support/technical/byproduct.affx?product=hug enefl HTH, Jim > > > Is there any way, I can get target sequences as FASTA > formatted files? > > Thanks > S. Peri > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor -- James W. MacDonald University of Michigan Affymetrix and cDNA Microarray Core 1500 E Medical Center Drive Ann Arbor MI 48109 734-647-5623 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.
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Thank you Dr. Symth (and Dr. MacDonald). As you have correctly suspected, the problem is with the input 'onebatch' which is a matrix. The matrix was actually extracted from the exprSet during an intermediate step, stored and used for subsequent analysis here. Is it a sensible suggestion for the lmFit() to set the rownames of the matrix as the gene names _if_ the class of object was matrix ? Might try later today to fudge to include a branch for is(object, "matrix") in the existing lmFit() code and post it. But is this worth the effort ? I presume there might be a few people who prefer to work with matrix of gene expression. E.g. those who only get the finalised dataset as the output of some public repositories. Or is it easier to convert a matrix to an exprSet and work from there ? Thank you. Regards, Adai On Sun, 2005-02-27 at 00:11 +1100, Gordon K Smyth wrote: > > Date: Fri, 25 Feb 2005 11:33:57 +0000 > > From: Adaikalavan Ramasamy <ramasamy@cancer.org.uk> > > Subject: [BioC] rownames in topTable and posterior probability > > To: BioConductor mailing list <bioconductor@stat.math.ethz.ch> > > > > topTable() in limma packages returns the row numbers and it would be > > useful to see the row names (i.e. Affy ID) instead. > > topTable() already does this, as can be seen from the case studies in the User's Guide. For > example, the Ecoli and Estrogen case studies show top tables with Affy IDs included automatically. > > > I am aware that I > > may supply the 'genelist' argument but help("topTable") says : > > > > genelist: data frame or character vector containing gene > > information. If not specified, this will be taken > > from the 'genes' component of 'fit'. > > This is not normally required. Have you not looked at the examples in the User's Guide? > > > My usual usage is as follows > > > > fit <- lmFit(onebatch, design) > > fit2 <- contrasts.fit( fit, cont.m ) > > fit2 <- eBayes(fit2) > > > > topTable(fit2) > > M t P.Value B > > 12358 -0.8636721 -7.585040 3.808592e-05 11.958486 > > 48048 -0.8765769 -7.400093 7.417187e-05 11.363358 > > ... > > > > But I found no genes component in fit via fit$genes or str(fit). Same > > goes for fit2. I doing something wrong ? > > You haven't told use what sort of object 'onebatch' is. If onebatch is an object from which gene > names can be extracted, e.g., an exprSet, then they should be included in 'fit'. If 'onebatch' > doesn't include gene names, you can't really expect them to be in fit. > > Gordon > > > Thank you. > > > > Regards, Adai > > >
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At 01:45 PM 28/02/2005, Adaikalavan Ramasamy wrote: >Thank you Dr. Symth (and Dr. MacDonald). > >As you have correctly suspected, the problem is with the input >'onebatch' which is a matrix. The matrix was actually extracted from the >exprSet during an intermediate step, stored and used for subsequent >analysis here. > >Is it a sensible suggestion for the lmFit() to set the rownames of the >matrix as the gene names _if_ the class of object was matrix ? Might try >later today to fudge to include a branch for is(object, "matrix") in the >existing lmFit() code and post it. But is this worth the effort ? That's a sensible suggestion which is easy to implement. I'll put it in the next version of limma. >I presume there might be a few people who prefer to work with matrix of >gene expression. E.g. those who only get the finalised dataset as the >output of some public repositories. In the case of public repositories, I doubt that the matrix will have rownames attached. Rownames are not in general a satisfactory way to store probe IDs because of the embarassment that non-unique rownames can potentially cause. The exprSet class gets away with storing probe IDs this way because exprSet is mostly used for Affy and Affy chips don't repeat probes. Gordon > Or is it easier to convert a matrix >to an exprSet and work from there ? > >Thank you. >Regards, Adai
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