Limma error - undefined columns selected

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Gordon Smyth 50k

@gordon-smyth

Last seen 9 minutes ago

WEHI, Melbourne, Australia

Dear Ankit, The error is caused by a bug in the function wtVariables() in limma. Try sourcing this replacement function into your session and see if it fixes the problem. Best wishes Gordon wtVariables <- function(x,fun) # Finds variable names in user-defined functions # Gordon Smyth # 3 Nov 2004. Last modified 2 Jan 2006. { x <- as.character(x) a <- deparse(fun) n <- length(x) ind <- logical(n) for (i in 1:n) { ind[i] <- as.logical(length(grep(protectMetachar(x[i]),a))) } x[ind] } At 10:00 PM 28/12/2005, bioconductor-request at stat.math.ethz.ch wrote: >Date: Tue, 27 Dec 2005 03:44:20 -0800 (PST) >From: Ankit Pal <pal_ankit2000 at="" yahoo.com=""> >Subject: [BioC] Limma error - undefined columns selected >To: bioconductor at stat.math.ethz.ch > > Hi All, > I'm using the latest version of limma to analyse a set of 3 gpr files. > The QC filter I have created is as follows > >myfun <- function(x,threshold=55){ > + okred <- abs(x[,"% > B635+2SD"]) > threshold > + okgreen <- abs(x[,"% > B532+2SD"]) > threshold > + okflag <- abs(x[,"Flags"]) > 0 > + okRGN <- abs(x[,"Rgn R2 (635/532)"] ) > 0.6 > + as.numeric(okgreen || okred || okflag || okRGN) > +} > > Onreading in the gpr files using > > >RG <- read.maimages(targets$FileName, source="genepix",wt.fun=myfun) > I get the following error > > Error in "[.data.frame"(x, , "% > B635+2SD") : > undefined columns selected > > I checked the columns and they are present in my gpr file. > > Why am I getting this error and how do I go about correcting it > > -Ankit

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ADD COMMENT • link updated 18.4 years ago by Gerhard Thallinger ▴ 180 • written 18.4 years ago by Gordon Smyth 50k

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Gerhard Thallinger ▴ 180

@gerhard-thallinger-1552

Last seen 6 weeks ago

Austria

Dear all, I am analyzing an experiment consisting of 4 one-channel hybridizations with two conditions and a technical replicate for each of them. I am using limma 2.4.4 (2005/11/29) under R 2.2.0 on Windows. The design matrix is as follows: 0h 2h 1 1 0 2 1 0 3 0 1 4 0 1 Since there are technical replicates the correlation between them should be taken into account: techrep <- c(1,1,2,2) corfit <- duplicateCorrelation(signal(anaexp), ndups = 1, block = techrep) fit <- lmFit(signal(anaexp), design, block = techrep, cor = corfit$consenus) The fit aborts with the following error: Error in backsolve(cholV, y, transpose = TRUE) : NA/NaN/Inf in foreign function call (arg 1) In addition: Warning messages: 1: NaNs produced in: sqrt(dfitted.values) 2: NaNs produced in: sqrt(dfitted.values) The error is probably a consequence of the warnings from the "corfit <-" step. What value would one expect for the consensus correlation ? Any ideas how to work around these error ? The fit without block and cor works flawlessly. Trying to define contrasts I encountered the following error messages: cont <- makeContrasts("2h-0h", levels = design) Error in parse(file, n, text, prompt) : syntax error in "2h" Obviously a digit as the first character is not allowed. Prepending a "T" before the condition solved this problem. Using a variable for the contrast lead to a different message: ctr <- "T2h-T0h" cont <- makeContrasts(ctr, levels = design) Error in eval(expr, envir, enclos) : object "ctr" not found This could be circumvented by using the following construct: cmd <- paste("cont <- makeContrasts(", ctr, ", levels = design)", sep = '"') eval(parse(text = cmd)) TIA for your help Gerhard

ADD COMMENT • link 18.4 years ago Gerhard Thallinger ▴ 180

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The problem is that in your design you have no biological replicates. If you use blocks, then you must have blockwise replication. You have no d.f. for testing. --Naomi At 01:29 PM 1/2/2006, Gerhard Thallinger wrote: >Dear all, > > I am analyzing an experiment consisting of 4 one-channel >hybridizations with two conditions and a technical replicate >for each of them. I am using limma 2.4.4 (2005/11/29) under >R 2.2.0 on Windows. The design matrix is as follows: > > 0h 2h >1 1 0 >2 1 0 >3 0 1 >4 0 1 > >Since there are technical replicates the correlation between them >should be taken into account: > > techrep <- c(1,1,2,2) > corfit <- duplicateCorrelation(signal(anaexp), ndups = 1, block = techrep) > fit <- lmFit(signal(anaexp), design, block = techrep, cor = > corfit$consenus) > >The fit aborts with the following error: > Error in backsolve(cholV, y, transpose = TRUE) : > NA/NaN/Inf in foreign function call (arg 1) > In addition: Warning messages: > 1: NaNs produced in: sqrt(dfitted.values) > 2: NaNs produced in: sqrt(dfitted.values) > >The error is probably a consequence of the warnings from the "corfit <-" step. >What value would one expect for the consensus correlation ? >Any ideas how to work around these error ? > >The fit without block and cor works flawlessly. Trying to define contrasts >I encountered the following error messages: > > cont <- makeContrasts("2h-0h", levels = design) > Error in parse(file, n, text, prompt) : syntax error in "2h" > >Obviously a digit as the first character is not allowed. Prepending a "T" >before the condition solved this problem. Using a variable for the contrast >lead to a different message: > > ctr <- "T2h-T0h" > cont <- makeContrasts(ctr, levels = design) > Error in eval(expr, envir, enclos) : object "ctr" not found > >This could be circumvented by using the following construct: > > cmd <- paste("cont <- makeContrasts(", ctr, ", levels = design)", > sep = '"') > eval(parse(text = cmd)) > >TIA for your help > >Gerhard > >_______________________________________________ >Bioconductor mailing list >Bioconductor at stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor Naomi S. Altman 814-865-3791 (voice) Associate Professor Dept. of Statistics 814-863-7114 (fax) Penn State University 814-865-1348 (Statistics) University Park, PA 16802-2111

ADD REPLY • link 18.4 years ago Naomi Altman ★ 6.0k

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