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meta-analysis

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Peevi Ijkl ▴ 170

@peevi-ijkl-4360

Last seen 10.4 years ago

Hilist i need some help regarding meta-analysis.I did the following.. pd <- read.AnnotatedDataFrame( ".txt", header=T, row.names=1, sep=";" ) pData(pd) expression_data <- ReadAffy( filenames = rownames (pData(pd)) ) expression_data rma_expression_data <-rma(expression_data) rma_data <- exprs(rma_expression_data) f1 <- function( x ) ( IQR(x) > 0.5 ) ff <- filterfun(f1) rma_filtered <- genefilter( rma_data, ff ) sum(rma_filtered) rma_data_selected <- rma_data [ rma_filtered, ] dim(rma_data) dim(rma_data_selected) cl <- as.numeric(pd$Condition == "" ) cl ##multtest resT <- mt.maxT(rma_data_selected, classlabel=cl, B=2000 ) ##Look at the first 10 probesets resT [1:10 , ] probe_sets <- rownames(resT) [1:100] ##Select the 1st 100 probsets resT7561<-resT[1:100,] resT7561 I tried doing venn mapping on this data,but am getting the following error Error in function (classes, fdef, mtable) : unable to find an inherited method for function "exprs", for signature "data.frame" I really dont know where am I going wrong. Also the meta-analysis clearly states that the original dataset is normalized and subsampled. Is there something am doing wrong? Please help thanks peevi [[alternative HTML version deleted]]

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ADD COMMENT • link updated 14.1 years ago by Steve Lianoglou ★ 13k • written 14.1 years ago by Peevi Ijkl ▴ 170

score 0 · Answer 1 · 2011-01-13

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Steve Lianoglou ★ 13k

@steve-lianoglou-2771

Last seen 23 months ago

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Hi, On Thu, Jan 13, 2011 at 6:36 PM, Peevi Ijkl <ipeevi at="" yahoo.com=""> wrote: > Hilist > i need some help regarding meta-analysis.I did the following.. > > pd <- read.AnnotatedDataFrame( ".txt", header=T, row.names=1, sep=";" ) > pData(pd) > expression_data <- ReadAffy( filenames = rownames (pData(pd)) ) > expression_data > rma_expression_data <-rma(expression_data) > rma_data <- exprs(rma_expression_data) > f1 <- function( x ) ( IQR(x) > 0.5 ) > ff <- filterfun(f1) > rma_filtered <- genefilter( rma_data, ff ) > sum(rma_filtered) > rma_data_selected <- rma_data [ rma_filtered, ] > dim(rma_data) > dim(rma_data_selected) > > cl <- as.numeric(pd$Condition == "" ) > cl > ##multtest > resT <- mt.maxT(rma_data_selected, classlabel=cl, B=2000 ) > > ##Look at the first 10 probesets > resT [1:10 , ] > probe_sets <- rownames(resT) [1:100] > > ##Select the 1st 100 probsets > resT7561<-resT[1:100,] > resT7561 > > I tried doing venn mapping on this data How? > ,but am getting the following error > Error in function (classes, fdef, mtable) ?: > ?unable to find an inherited method for function "exprs", for signature > "data.frame" I think the key point here is to figure out where this error is occurring. Go back to the 20 or so lines of codes that you pasted, and look at the 6th line: rma_data <- exprs(rma_expression_data) I guess this error must be happening there, right? If so, then your error is on or before that line. Furthermore, there should be even more errors that follow that one, no? -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology ?| Memorial Sloan-Kettering Cancer Center ?| Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact

ADD COMMENT • link 14.1 years ago Steve Lianoglou ★ 13k

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Hey steve I thought the same..so i tried another approach by creating an expression object at the end of the filtering..and then doing the venn mapping..but still i get the same error..any ideas?? thanks peevi ________________________________ From: Steve Lianoglou <mailinglist.honeypot@gmail.com> Cc: bioconductor <bioconductor@stat.math.ethz.ch> Sent: Thu, January 13, 2011 8:17:13 PM Subject: Re: [BioC] meta-analysis Hi, > Hilist > i need some help regarding meta-analysis.I did the following.. > > pd <- read.AnnotatedDataFrame( ".txt", header=T, row.names=1, sep=";" ) > pData(pd) > expression_data <- ReadAffy( filenames = rownames (pData(pd)) ) > expression_data > rma_expression_data <-rma(expression_data) > rma_data <- exprs(rma_expression_data) > f1 <- function( x ) ( IQR(x) > 0.5 ) > ff <- filterfun(f1) > rma_filtered <- genefilter( rma_data, ff ) > sum(rma_filtered) > rma_data_selected <- rma_data [ rma_filtered, ] > dim(rma_data) > dim(rma_data_selected) > > cl <- as.numeric(pd$Condition == "" ) > cl > ##multtest > resT <- mt.maxT(rma_data_selected, classlabel=cl, B=2000 ) > > ##Look at the first 10 probesets > resT [1:10 , ] > probe_sets <- rownames(resT) [1:100] > > ##Select the 1st 100 probsets > resT7561<-resT[1:100,] > resT7561 > > I tried doing venn mapping on this data How? > ,but am getting the following error > Error in function (classes, fdef, mtable) : > unable to find an inherited method for function "exprs", for signature > "data.frame" I think the key point here is to figure out where this error is occurring. Go back to the 20 or so lines of codes that you pasted, and look at the 6th line: rma_data <- exprs(rma_expression_data) I guess this error must be happening there, right? If so, then your error is on or before that line. Furthermore, there should be even more errors that follow that one, no? -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact [[alternative HTML version deleted]]

ADD REPLY • link 14.1 years ago Peevi Ijkl ▴ 170

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Hi, On Thu, Jan 13, 2011 at 8:29 PM, Peevi Ijkl <ipeevi at="" yahoo.com=""> wrote: > Hey steve > I thought the same..so i tried another approach by creating an expression > object at the end of the filtering..and then doing the venn mapping..but > still i get the same error..any ideas?? Sorry, I'm not understanding what you are telling me. My question was when *specifically* did you get the error that you report. That is to say, after which command of the 20 that you showed us did this error pop up: >> Error in function (classes, fdef, mtable) ?: >> ?unable to find an inherited method for function "exprs", for signature >> "data.frame" -- Steve Lianoglou Graduate Student: Computational Systems Biology ?| Memorial Sloan-Kettering Cancer Center ?| Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact

ADD REPLY • link 14.1 years ago Steve Lianoglou ★ 13k

score 0 · Answer 2 · 2011-01-13

Peevi: (1) please keep all correspondence on list so that all may benefit from any help provided; and On Thu, Jan 13, 2011 at 10:50 PM, Peevi Ijkl <ipeevi at="" yahoo.com=""> wrote: > sorry..yes it showed up at the end of the code that i posted (2) Sorry, I'm lost. I don't really see how that can be the case. Are you perhaps `source`-ing an entire file or something and therefore missing where the error is happening. Or trying to copy a code chunk from a text editor, and pasting it all into an R session? Or are you really running each line out at a time and waiting for each result before you try to run the next line? You're saying that after you run this line: ##Select the 1st 100 probsets R> resT7561<-resT[1:100,] R> resT7561 You get this error: >> Error in function (classes, fdef, mtable) : >> unable to find an inherited method for function "exprs", for signature >> "data.frame" ? -- Steve Lianoglou Graduate Student: Computational Systems Biology ?| Memorial Sloan-Kettering Cancer Center ?| Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact