Error In Function Classes Def Mtable
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to find an inherited method for function "indexProbes", for signature "exprSet", "character" 0 8.6 years
Error In (function (classes, Fdef, Mtable) : Unable To Find An Inherited Method For Function
ago by Suprabhath Reddy Gajjala • 20 Suprabhath Reddy Gajjala • error in (function (classes, fdef, mtable) in r 20 wrote: Hello Everyone, I am writing programs in R from 7 months and I am xlconnect able to solve most of the errors/issues except for this current post. My Task is to read a Microsoft Excel file(textE_to_affy.csv) which contains the Microarray Expression Values collected from the Illumina Microarray experiment. These collected intensity values need to be normalized(Rank Invariant Normalization) by using the R function "normalize.AffyBatch.invariantset()". Since the normalize.AffyBatch.invariantset() method requires the input argument to be an AffyBatch Object, I used the read.exprSet() method to convert the intensity values present in the (textE_to_affy.csv) file into an AffyBatch Object as follows: > testFile <- tempfile() >textAffy<-read.table("textE_to_affy.csv",header=TRUE,sep=",",row.name s=1) > textAffy Sample1 Sample2 Sample3 GI_10047089-S -6.100 -5.12500 -5.61250 GI_10047091-S 10.725 9.70625 10.21562 GI_10047093-S 1392.100 1378.70000 1385.40000 GI_10047099-S 264.925 260.98125 262.95312 GI_10047103-S 5315.675 5412.01875 5363.84688 GI_10047105-S 21.750 22.53750 22.14375 > write.table(TA,testFile,quote = FALSE, sep = "\t", row.names = TRUE, col.names = TRUE) > testFile [1] "C:\\DOCUME~1\\Jaswanth\\LOCALS~1\\Temp\\RtmpXrUE8T\\file2ea6bb3" > eSet <- read.exprSet(testFile) Warning messages: 1: read.exprSet is deprecated, use readExpresionSet instead 2: read.phenoData is deprecated, use read.AnnotatedDataFrame instead 3: The phenoData class is deprecated, use AnnotatedDataFrame (with ExpressionSet) instead 4: The exprSet class is deprecated, use ExpressionSet instead 5: The exprSet class is deprecated, use ExpressionSet instead 6: The exprSet class is deprecated, use ExpressionSet instead 7: The exprSet class is deprecated, use ExpressionSet instead 8: The exprSet class is deprecated, use ExpressionSet instead 9: The exprSet class is deprecated, use ExpressionSet instead > > eSet Expression Set (exprSet) with 6 genes 3 samples phenoData object with 1 variables and 3 cases varLabels sample: arbitrary numbering Warning
Sign in Pricing Blog Support Search GitHub This repository Watch 35 Star 100 Fork 60 joey711/phyloseq Code Issues 86 Pull requests 8 Projects 0 Wiki Pulse Graphs New issue Error in function (classes, fdef, mtable) #147 Closed tboonf opened this Issue Sep 29, 2012 · 5 comments Projects None yet Labels None yet Milestone No milestone Assignees No one assigned 2 participants tboonf commented Sep 29, 2012 Hi, I received the following error message as I https://support.bioconductor.org/p/21655/ was trying to plot a tree: plot_tree(test) Error in function (classes, fdef, mtable) : unable to find an inherited method for function "otu_table", for signature "phylo" Does anyone have any idea what might have gone wrong? Please let me know. Thanks :) Owner joey711 commented Sep 30, 2012 You have to have a tree to plot a https://github.com/joey711/phyloseq/issues/147 tree. Do you have a tree file somewhere? You can also calculate a tree using functions in ape, phangorn, etc. Functions in the phyloseq package that are going to do something with a tree require that a tree already be calculated, and that the tree is a "phylo"-class, as defined by the ape package. Owner joey711 commented Sep 30, 2012 Also, if you had a "phylo" object available and wanted to do something with it in the phyloseq package, chances are it is because you also have an "otu_table" and other metadata with with which you want to annotate your graphic. In that case, you need to group them together in a formal way, using the phyloseq function. joey711 closed this Sep 30, 2012 tboonf commented Sep 30, 2012 Problem is not resolved, unfortunately. This is what I did: my_otu_table<- read.table(file="otu_table1.csv", header=T, sep=",") my_otu_table otu_table(my_otu_table, taxa_are_rows=TRUE,errorIfNULL=TRUE) OTU Table: [39 taxa and 3 samples] taxa are rows sampledata<- read.table(file="sampledata.csv", header=T, sep=",") sampleData(sampledata, errorIfNULL=TRUE) Sample Data: [3 samples by 3 sample variables]:
here for a quick overview of the site Help Center Detailed answers to any questions you might have Meta Discuss the workings and policies of this site About Us Learn more about Stack Overflow the http://stackoverflow.com/questions/26587659/error-in-xlconnect company Business Learn more about hiring developers or posting ads with us Stack Overflow Questions Jobs Documentation Tags Users Badges Ask Question x Dismiss Join the Stack Overflow Community Stack Overflow is a community of 4.7 million programmers, just like you, helping each other. Join them; it only takes a minute: Sign up Error in XLConnect up vote 4 down vote favorite I am trying to import an excel sheet into r. error in I used the following code: x <- loadWorkbook("x.xlsx") b <- readWorksheet(x, sheet="b") The first line works fine, however, running the second gives the following error: Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘readWorksheet’ for signature ‘"jobjRef", "character"’ I have no missing values in that sheet. For the purpose of reproducing, download trial.xlsx from https://github.com/ahmedfsalhin/1stpaper. system info: Yosemite operating system. r xlconnect share|improve this question edited error in (function Oct 27 '14 at 16:42 asked Oct 27 '14 at 12:31 Ahmed Salhin 536522 It would be very helpful to post a link to an example workbook that causes this. That said, Yosemite is brand-new; you may need to reinstall Java and/or wait for new CRAN builds of Rjava . –Carl Witthoft Oct 27 '14 at 14:07 @CarlWitthoft I have just updated the question with a link to excel file to reproduce. –Ahmed Salhin Oct 27 '14 at 16:42 @CarlWitthoft I did update to Java Development Kit 8 (JDK 8) and after installing the XLConnect again, it works fine now. –Ahmed Salhin Oct 27 '14 at 17:37 @CarlWitthoft Sorry it is not the Java. It is xlsx package that make the confusion. –Ahmed Salhin Oct 27 '14 at 17:47 add a comment| 3 Answers 3 active oldest votes up vote 6 down vote accepted It appears the "root cause" is that you should add code to specify both the function and the package it belongs to. Type XLConnect::loadWorkbook to select the one you want in this case. There's no 'confusion,' or random selection of duplicated function names in R. The choice depends on the load order of all loaded packages. Use search() to see the order in which