Thanks! Davis. However, this problem was resolved in the developing version. It should run well if you use the developing version 1.7.xx. Anyway, thanks for reporting the problem. Have a nice day, Pan On 10/21/08 5:00 AM, "bioconductor-request at stat.math.ethz.ch" <bioconductor-request at="" stat.math.ethz.ch=""> wrote: > Date: Mon, 20 Oct 2008 14:51:46 -0500 > From: "Davis, Wade" <davisjwa at="" health.missouri.edu=""> > Subject: [BioC] Possible problem with lumi function > addControlData2lumi and proposed solution > To: <bioconductor at="" stat.math.ethz.ch=""> > Message-ID: > <09E4AABB118D2C47AEDFC6210BF1DEA902F2A702 at UM- XMAIL02.um.umsystem.edu> > Content-Type: text/plain > > Dear Pan Du et al (and other bioconductoRs): > > > > First, let me say that I have been using the lumi package for a few > years now, and I appreciate the time and effort it takes to maintain a > package. I am very grateful. > > > > I just recently received some data from Illumina's Human HT-12 (V3) > chip. It is the first time I've used it with lumi. I decided to finally > take advantage of the controlData slot by using the addControlData2lumi > function. However, when using it, I got the following error message. > > > >> addControlData2lumi(controlFile, eth.lumi) > > [1] "Inputting the data ..." > > [1] "Adding nuID to the data ..." > > Error in addControlData2lumi(controlFile, eth.lumi) : > > SampleID does not match up between controlData and x.lumi! > > In addition: Warning message: > > In addNuId2lumi(x.lumi, lib = lib) : > > Please provide the annotation file or lumi annotation library! > > > > I am primarily concerned about the message: "SampleID does not match up > between controlData and x.lumi!" > > I had the problem with both lumi 1.6.3 and 1.4.0. > > > > Digging into the function, it appears that the creation of the > controlData dataframe is causing the problem. > > > > function (controlData, x.lumi) > > { > > if (missing(x.lumi) || missing(controlData)) > > stop("Both controlData and x.lumi are required!") > > if (is.character(controlData)) { > > controlFile <- controlData > > allControlInfo <- lumiR.batch(controlFile, lib = NULL, > > checkDupId = FALSE) > > controlData <- as.data.frame(exprs(allControlInfo)) > > controlType <- > as.character(pData(featureData(allControlInfo))$TargetID) > > ProbeID <- > as.character(pData(featureData(allControlInfo))$ProbeID) > > controlData <- data.frame(controlType = controlType, > > ProbeID = ProbeID, controlData) > > } > > if (is.matrix(controlData)) > > controlData <- as.data.frame(controlData) > > if (is(controlData, "data.frame")) { > > sampleID <- as.character(pData(phenoData(x.lumi))$sampleID) > > if (is.null(sampleID)) > > sampleID <- sampleNames(x.lumi) > > controlSampleID <- names(controlData) > > if ("TargetID" %in% controlSampleID) { > > controlSampleID[controlSampleID == "TargetID"] <- > "controlType" > > } > > if (all(sampleID %in% controlSampleID)) { > > x.lumi at controlData <- controlData[, c("controlType", > > "ProbeID", sampleID)] > > } > > else { > > sampleIDInfo <- strsplit(sampleID, split = "_") > > newID <- NULL > > temp <- lapply(sampleIDInfo, function(x) { > > newID <<- c(newID, paste(x[1:2], collapse = "_")) > > }) > > if (all(newID %in% controlSampleID)) { > > x.lumi at controlData <- controlData[, c("controlType", > > "ProbeID", newID)] > > } > > else { > > stop("SampleID does not match up between controlData and > x.lumi!") > > } > > } > > names(x.lumi at controlData) <- c("controlType", "ProbeID", > > sampleNames(x.lumi)) > > } > > else { > > stop("Input data type is not supported!") > > } > > return(x.lumi) > > } > > > > When controlData is first defined as > > controlData <- as.data.frame(exprs(allControlInfo)) > > the variable names from my data are: > > [1] "4421321204_A" "4421321204_B" "4421321204_C" "4421321204_D" > "4421321204_E" "4421321204_F" > > [7] "4421321204_G" "4421321204_H" "4421321204_I" "4421321204_J" > "4421321204_K" "4421321204_L" > > which are just the chip names. > > > > After this line: > > controlData <- data.frame(controlType = controlType, > > ProbeID = ProbeID, controlData) > > the variable names from my data become: > > 1] "controlType" "ProbeID" "X4421321204_A" "X4421321204_B" > "X4421321204_C" "X4421321204_D" > > [7] "X4421321204_E" "X4421321204_F" "X4421321204_G" "X4421321204_H" > "X4421321204_I" "X4421321204_J" > > [13] "X4421321204_K" "X4421321204_L" > > As you can see, the chip names now have the letter X appended. Thus, > when the function compares controlSampleID to newID, it says they do not > match. > > > > The X prefix on the chip names comes from the make.names function being > employed because the default behavior of data.frame is to have > check.names=T, which triggers make.names. I modified > addControlData2lumi() by adding check.names=F as such: > > controlData <- data.frame(controlType = controlType, > > ProbeID = ProbeID, controlData,check.names=F) > > > > Then the function works fine. > > > > So I suggest making this change, although I don't know what unintended > behavior this could cause with other lumi functions. If the change is > made, more code might be needed to make sure that chip names are not > duplicated. > > > > I hope this message has been useful, and that I have not overlooked > other messages on this topic. Thank for your time. > > > > Regards, > Wade > > > > > > J. Wade Davis, PhD > > University of Missouri > >