R Error In Function Classes Fdef Table
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to find an inherited method for function "indexProbes", for signature "exprSet", "character" 0 8.6 years ago by error in (function (classes, fdef, mtable) in r Suprabhath Reddy Gajjala • 20 Suprabhath Reddy Gajjala • 20 wrote: Hello
Error In (function (classes Fdef Mtable) Unable To Find An Inherited Method For Function
Everyone, I am writing programs in R from 7 months and I am able to solve most unable to find an inherited method for function ‘dbconnect’ for signature ‘"character"’ 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 messages: 1: The exprSet class is deprecated, use ExpressionSet instead 2: The exprSet class is de
setMethod for "[" Next message: [R] Error in function (classes, fdef, mtable): unable to find an inherited method for function "indexProbes", for signature "exprSet", "character" Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] Hello Everyone, I am writing programs in R from 7 months and I am able to solve most of https://support.bioconductor.org/p/21655/ 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 https://stat.ethz.ch/pipermail/r-help/2008-March/157722.html 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.names=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 exprSe
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 http://stackoverflow.com/questions/16738822/unable-to-access-gsm-list-in-geoquery-r more about Stack Overflow the company Business Learn more about hiring developers or http://stackoverflow.com/questions/29935512/scraping-multiple-table-out-of-webpage-in-r 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 6.2 million programmers, just like you, helping each other. Join them; it only takes a minute: Sign up Unable to access GSM List in GEOquery R up vote error in 2 down vote favorite I am working with a GSE set that contains 2 series matrices and would like to covert the whole thing to an expression set so that I can work with it in Limma. I have loaded the GSE using the following command: > gse <- getGEO('GSE16560', GSEMatrix = T) When I attempt to access the GSM list to check the platforms I get the error in (function following error: > GSMList(gse) Error in (function (classes, fdef, mtable) : unable to fin an inherited method for function 'GSMList' for signature '"list"' So far, I checked the dimensions of the gse object and it was NULL so that doesn't help. Also, it's not a list. It also throws the same error when I call 'Meta(gse)'. I'm relatively new to these data structures and R in general so if someone could point me in the right direction it would be a huge help. r geo bioconductor share|improve this question asked May 24 '13 at 15:43 Aidan Quinn 234 Asking on the Bioconductor mailing list is appropriate for Bioconductor packages like GEOquery. Be sure to include the output of sessionInfo() so that others on the list know the version R and packages you are using. –Martin Morgan May 24 '13 at 20:56 @MartinMorgan thanks, this is a great resource that I was not previously aware of :) –Aidan Quinn May 28 '13 at 19:11 add a comment| 2 Answers 2 active oldest votes up vote 1 down vote your 'gse' object is a list of two expression sets. library(GEOquery) gse <- getGEO('GSE16560', GSEMatrix = T) class(gse) # [1] "list
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 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 6.2 million programmers, just like you, helping each other. Join them; it only takes a minute: Sign up Scraping multiple table out of webpage in R up vote 1 down vote favorite I am trying to pull mutual funds data into R, My way of code works for single table but when there are multiple tables in a webpage, it doesn't work. Link - https://in.finance.yahoo.com/q/pm?s=115748.BO My Code url <- "https://in.finance.yahoo.com/q/pm?s=115748.BO" library(XML) perftable <- readHTMLTable(url, header = T, which = 1, stringsAsFactors = F) but i am getting an error message. Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘readHTMLTable’ for signature ‘"NULL"’ In addition: Warning message: XML content does not seem to be XML: 'https://in.finance.yahoo.com/q/pm?s=115748.BO' My Question is How to pull a specific table out of this webpage? How to pull all tables out of this webpage? when there are multiple links, what would be the easy way to pull specific table from each those webpages Ahttps://in.finance.yahoo.com/q/pm?s=115748.BO Ahttps://in.finance.yahoo.com/q/pm?s=115749.BO Ahttps://in.finance.yahoo.com/q/pm?s=115750.BO Remove "A" From the link, while using the link. r data.table screen-scraping share|improve this question edited Oct 19 '15 at 18:11 Brian Tompsett - 汤莱恩 3,103132775 asked Apr 29 '15 at 6:00 Ananya Pandey 225 add a comment| 2