[BioC] Possible problem with lumi function addControlData2lumi and proposed solution

[Pan Du]

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
> 
>