Error In .data.frame Obj Columns A Undefined Columns Selected
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columns [[a]]): undefined columns selected" 0 5.2 undefined columns selected error in r years ago by Paz Tapia Ramirez • 150 Paz error in `[.data.frame`(frame, predictors) : undefined columns selected Tapia Ramirez • 150 wrote: Hello, I've been working with the package of bioconductor error in `[.data.frame`(y.data, , mediator) : undefined columns selected Agi4x44PreProcess, but reads data error says "Error in` [. Data.frame `(obj,, columns [[a]]): undefined columns selected" My file is targets.txt: FileName Treatment GErep Subject undefined columns selected r predict Array 1.txt ISO 1 Subj 1 2.txt ISO 2 Subj 1 3.txt ISO 1 Subj 1 4.txt ISO 2 Subj 1 And un example of head of 1.txt file is FEATURES FeatureNum Row Col accessions chr_coord SubTypeMask SubTypeName ProbeUID ControlType ProbeName GeneName SystematicName Description PositionX PositionY gSurrogateUsed gIsFound
Error In View Undefined Columns Selected
gProcessedSignal gProcessedSigError gNumPixOLHi gNumPixOLLo gNumPix gMeanSignal gMedianSignal gPixSDev gPixNormIQR gBGNumPix gBGMeanSignal gBGMedianSignal gBGPixSDev gBGPixNormIQR gNumSatPix gIsSaturated gIsLowPMTScaledUp gIsBGNonUnifOL gIsFeatPopnOL gIsBGPopnOL IsManualFlag gBGSubSignal gBGSubSigError gIsPosAndSignif gPValFeatEqBG gNumBGUsed gIsWellAboveBG gBGUsed gBGSDUsed ErrorModel gSpatialDetrendIsInFilteredSet gSpatialDetrendSurfaceValue SpotExtentX SpotExtentY gNetSignal gMultDetrendSignal gProcessedBackground gProcessedBkngError IsUsedBGAdjust gInterpolatedNegCtrlSub gIsInNegCtrlRange gIsUsedInMD Tab-separated [[alternative HTML version deleted]] agi4x44preprocess ADD COMMENT • link • Not following Follow via messages Follow via email Do not follow modified 5.2 years ago by Paz Tapia Ramirez • 40 • written 5.2 years ago by Paz Tapia Ramirez • 150 0 5.2 years ago by Paz Tapia Ramirez • 40 Paz Tapia Ramirez • 40 wrote: Hello, I've been working with the package of bioconductor Agi4x44PreProcess, but reads data error says "Error in` [. Data.frame `(obj,, columns [[a]]): undefined columns selected" My file is targets.txt: FileName Treatment GErep Subject Array 1.txt ISO 1 Subj 1 2.tx
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Error In Data Frame Object Not Found
about hiring developers or posting ads with us Stack Overflow Questions Jobs Documentation Tags Users shiny undefined columns selected Badges Ask Question x Dismiss Join the Stack Overflow Community Stack Overflow is a community of 4.7 million programmers, just like you, helping error in data.frame arguments imply differing number of rows each other. Join them; it only takes a minute: Sign up Error in data frame undefined columns selected up vote 1 down vote favorite I've been working on an assignment where I have to read in some csv https://support.bioconductor.org/p/40541/ files from a directory "specdata". The files are very similar in that there are 332 titled 001.csv - 332.csv. They have consistent columns and headers, if that matters. I believe I'm close but am tripping up with the above error message " Error in [.data.frame(data1, good) : undefined columns selected" I had expected a data frame to load with all the data specified by the subset of files in id parameter. pollutantmean <- function(directory, pollutant, id = http://stackoverflow.com/questions/23666611/error-in-data-frame-undefined-columns-selected 1:332) { files <- list.files(directory) subsetFiles <- files[id] for (i in subsetFiles) { filepaths <- paste(directory,"/",i, sep='') data1 <- read.csv(filepaths) } data1 good <- complete.cases(data1) data2 <- data1[good] data2 } # test it out and ignore middle parameter for now pollutantmean("specdata", "pass", 1:3) r share|improve this question edited Oct 23 '14 at 13:29 Cerbrus 35.3k66094 asked May 14 '14 at 23:04 Doug Fir 2,732164189 add a comment| 2 Answers 2 active oldest votes up vote 5 down vote accepted Are you meaning? data2 <- data1[good,] With data1[good] you're selecting columns in a wrong way (using a logical vector of complete rows). Consider that parameter pollutant is not used; is it a column name that you want to extract? if so it should be something like data2 <- data1[good, pollutant] Furthermore consider that you have to rbind the data.frames inside the for loop, otherwise you get only the last data.frame (its completed.cases) And last but not least, i'd prefer generating filenames eg with id <- 1:322 paste0( directory, "/", gsub(" ", "0", sprintf("%3d",id)), ".csv") A little modified chunk of ?sprintf The string fmt (in our case "%3d") contains normal characters, which are passed through to the output string, and also conversion specifications which operate on the arguments provided through .... The allowed conversion specifications start with a % and end with one of the letters in the set aAdife
function in timecourse Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] Er, why are you specifying sep="," for tab-delimited file? This file reads fine in all versions of limma using default settings. Gordon At 10:44 PM 17/10/2005, Ye, Bin https://stat.ethz.ch/pipermail/bioconductor/2005-October/010540.html wrote: >Hi, Gordon, > >Thank you for your reply! I feel it's more likely a limma problem, see my >code below: > >RG <- read.maimages("03_122589_0693_1_Cont_PMT400_r40_g10.gpr", >source="genepix", sep=",") >Error in "[.data.frame"(obj, , columns[[a]]) : > undefined columns selected > >The gpr file was generated by GenePix 6. I'm attaching the file, in case >you need it for debugging. > >BTW, my system is: R 2.1.1, limma 2.0.8 and limma 2.2.0 both used, both >gave the same error as above. > > >Bin > error in > >-----Original Message----- >From: Gordon Smyth [mailto:smyth at wehi.edu.au] >Sent: Sat 10/15/2005 6:20 AM >To: Ye, Bin >Cc: bioconductor at stat.math.ethz.ch; Saroj Mohapatra >Subject: Re: [BioC] Limma read GenePix version 6 file > >limma has been well tested with GenePix 6 and there should be no problem. >Specifying columns explicitly should not be required. If you believe >there's a limma error, please give the code you used so that we can debug. > >BTW, the columns that Saroj specified (all medians) can now undefined columns selected be given as > > source="genepix.median" > >Gordon > > >Date: Fri, 14 Oct 2005 16:11:25 -0400 > >From: "Ye, Bin"