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Question: heatmap-exprs error
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gravatar for Rao,Xiayu
4.4 years ago by
Rao,Xiayu530
United States
Rao,Xiayu530 wrote:
Hello, Thank you in advance for answering my question!! I encountered an error when I intended to draw a heatmap based on the output from limma package. I selected those genes with low adjusted p values, and use their expression information to draw a heatmap. It turned out that the exprs function does not work. Really do not know how to solve this. Please help me out! Thanks a lot! > selected <- p.adjust(contrasts.fit$p.value[, 1]) <0.05 > selectgenes <- y[selected,] > heatmap(exprs(selectgenes)) Error in (function (classes, fdef, mtable) : unable to find an inherited method for function 'exprs' for signature '"EList"' > exprs(selectgenes) Error in (function (classes, fdef, mtable) : unable to find an inherited method for function 'exprs' for signature '"EList"' Thanks, Xiayu [[alternative HTML version deleted]]
ADD COMMENTlink modified 4.4 years ago by Wolfgang Huber13k • written 4.4 years ago by Rao,Xiayu530
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gravatar for Wolfgang Huber
4.4 years ago by
EMBL European Molecular Biology Laboratory
Wolfgang Huber13k wrote:
Dear Xiayu while it is quite legitimate to consider this an error, it in fact happens by design. limma's EList class does not support the 'exprs' accessor. You could try library("limma") class ? EList Best wishes Wolfgang On Jun 20, 2013, at 10:41 pm, "Rao,Xiayu" <xrao at="" mdanderson.org=""> wrote: > Hello, > > Thank you in advance for answering my question!! > > I encountered an error when I intended to draw a heatmap based on the output from limma package. I selected those genes with low adjusted p values, and use their expression information to draw a heatmap. It turned out that the exprs function does not work. Really do not know how to solve this. Please help me out! Thanks a lot! > >> selected <- p.adjust(contrasts.fit$p.value[, 1]) <0.05 >> selectgenes <- y[selected,] >> heatmap(exprs(selectgenes)) > Error in (function (classes, fdef, mtable) : > unable to find an inherited method for function 'exprs' for signature '"EList"' > >> exprs(selectgenes) > Error in (function (classes, fdef, mtable) : > unable to find an inherited method for function 'exprs' for signature '"EList"' > > Thanks, > Xiayu > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD COMMENTlink written 4.4 years ago by Wolfgang Huber13k
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