Error In Function Classes Fdef Mtable
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to find an inherited method for function "indexProbes", for signature "exprSet", "character" 0
Error In (function (classes, Fdef, Mtable) In R
8.6 years ago by Suprabhath Reddy Gajjala • 20 Suprabhath error in (function (classes fdef mtable) unable to find an inherited method for function Reddy Gajjala • 20 wrote: Hello Everyone, I am writing programs in R from 7 months
Unable To Find An Inherited Method For Function Summary
and I am 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 obj
faq • rss Community Log In Sign Up Add New Post Question: Error in (function (classes, fdef, mtable): unable to find an inherited method for function ‘annotation’ for signature ‘"character 0 2.4 years ago by ira_grich • 0 United States ira_grich • 0 wrote: INSILICOMERGING: Run with no additional merging technique... Error in (function (classes, fdef, mtable): unable to find an inherited method for function ‘annotation’ for signature ‘"character" insilicomerging • 4.4k views ADD COMMENT • link • Not following Follow via messages Follow via email Do not follow written 2.4 years ago by ira_grich • 0 And the command https://support.bioconductor.org/p/21655/ that produced this was...? I'm guessing you ran merge("esets") or something like that, instead of merge(esets), but I pretty much have to read your mind to know what you're actually doing. ADD REPLY • link written 2.4 years ago by Devon Ryan ♦ 56k Hi Devon, I am using "inSilicoMerging" and getting an error message: Error in (function (classes, fdef, mtable) : unable to find an inherited method for https://www.biostars.org/p/101868/ function ‘annotation’ for signature ‘"character"’ I Use R version 3.1.0 ; Bioconductor version 2.14; on Mac OS X 10.7.5 My steps: (1) # From ArrayExpress I download 2 raw zip files: E-GEOD-52763 (E-GEOD-52763.raw.1.zip) and E_GEOD-45006 (E-GEOD-45006.raw.1.zip) # code library(affy) library(annaffy) ReadCell = ReadAffy() Norm.data = rma(ReadCell) eset1<-Norm.data # code eset2<-Norm.dat # code: library(inSilicomerging >esets=list(eset1,eset2) > eset_FRMA = merge(esets) INSILICOMERGING: Run with no additional merging technique... Error in (function (classes, fdef, mtable): unable to find an inherited method for function ‘annotation’ for signature ‘"character"’ or any other gave me the same error message: >eset_BMC = merge(esets, method="BMC") > eset_NULL = merge(esets, method=NULL, norm="FRMA", features = "GENE"); > eset_12 = merge(esets, method=NULL, norm="ORIGINAL"); ADD REPLY • link written 2.4 years ago by ira_grich • 0 I'm using virtualArray package and I got the same error!!! how you solve your problem? ADD REPLY • link written 16 months ago by Shamim Sarhadi • 170 Please log in to add an answer. Similar posts • Search » INSILICOMERGING: Error in (function (classes, fdef, mtable) Hi , I am using Bioconductor/R and "inSilicoMerging" package. I got an error message: INSILICOME... Normalization of microarray data? Please help me to pinpoint the error..? featureData: none experimentData: use'experiment... ERROR in loading data through rma hello DEAR!
faq • rss Community Log In Sign Up Add New Post Question: INSILICOMERGING: Error in (function (classes, fdef, mtable) 0 2.4 years ago by ira_grich • 0 https://www.biostars.org/p/101755/ United States ira_grich • 0 wrote: Hi , I am using Bioconductor/R and "inSilicoMerging" package. I got an error message: INSILICOMERGING: Run with no additional merging technique... Error in (function (classes, fdef, mtable): unable to find https://r-forge.r-project.org/forum/forum.php?thread_id=27708&forum_id=4325&group_id=1420 an inherited method for function ‘annotation’ for signature ‘"character" Please tell me what does this message means? Tnx My steps: (1) download E-GEOD-52763 (E-GEOD-52763.raw.1.zip) and E_GEOD-45006 (E-GEOD-45006.raw.1.zip) (2) #code library(affy) library(annaffy) ReadCell error in = ReadAffy() Norm.data = rma(ReadCell) (3) # code: >eset1<-Norm.data >eset2<-Norm.data (4) # code: library(inSilicoMerging) >esets= list(eset1,eset2) > eset_FRMA = merge(esets) INSILICOMERGING: Run with no additional merging technique... Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘annotation’ for signature ‘"character"’ same error message: >eset_BMC = merge(esets, method="BMC") R • 1.6k views ADD COMMENT • link • Not following Follow classes fdef mtable via messages Follow via email Do not follow modified 2.3 years ago by Biostar ♦♦ 0 • written 2.4 years ago by ira_grich • 0 Have you tried this? http://comments.gmane.org/gmane.science.biology.informatics.conductor/37624 ADD REPLY • link modified 2.3 years ago • written 2.3 years ago by dasdevashishdas • 110 Please log in to add an answer. Similar posts • Search » Error in (function (classes, fdef, mtable): unable to find an inherited method for function ‘annotation’ for signature ‘"character INSILICOMERGING: Run with no additional merging technique... Error in (function (classes, fdef, ... RMA problem in affy package Hello, I wrote following R code to analyze affymeterix microarray data library(BiocGenerics) ... Normalization of microarray data? Please help me to pinpoint the error..? featureData: none experimentData: use'experiment... ERROR in loading data through rma hello DEAR! i am facing problem in loading data through rma in R. when i have run the command ... ORF lengths using Yeast Annotation package Hi, I am trying to find out length of Yeast ORF. Where is my mistake? > sacCer3Length <- ... Human gene2.0ST analysis using R Dear all, I'm trying to process CEL file from Human gene2.0 ST array to make