Error in estimateCellCounts

[MeganBreitbach]

I get an error regarding the slot names for the RGset when implementing my code to determine cell counts from methylEPIC data. Could anyone help me out here?

Read in data

targets<-read.metharray.sheet(base = "~/Documents/IDATS", pattern = "csv$", ignore.case = TRUE, recursive = TRUE, verbose = TRUE )

path<-"~/Documents/IDATS" RGset<-read.metharray.exp(base = path, targets = targets, extended = FALSE,recursive = FALSE, verbose = FALSE, force = FALSE) pData<- pData(RGset) pData$Sample_Name <- as.character(pData$Sample_Name) pData(RGset) <- pData

require(FlowSorted.Blood.450k)

cellCounts <- estimateCellCounts(RGset)

Error in colData(referenceRGset) : no slot of name "colData" for this object of class "RGChannelSet" Error in nrow(x@elementMetadata) : no slot of name "elementMetadata" for this object of class "RGChannelSet"

[kasperdanielhansen]

I think you're using the devel version of minfi, right? I think this is because we have changed the underlying class structures. We have updated the minfiData / minfiDataEPIC packages to support this, but we have not yet updated the FlowSorted.XX packages (well, I kind of forgot to be honest). You can update "old" objects to the new format by running updateObject().

Unfortunately, due to how estimateCellCounts is coded, you need to update the data in the package; it cannot be overridden by a user. So you'll have to wait until we fix this, which I hope will happen by the end of this week.

On Mon, Dec 5, 2016 at 10:05 PM, Megan notifications@github.com wrote:

I get an error regarding the slot names for the RGset when implementing my code to determine cell counts from methylEPIC data. Could anyone help me out here?

Read in data

targets<-read.metharray.sheet(base = "~/Documents/IDATS", pattern = "csv$", ignore.case = TRUE, recursive = TRUE, verbose = TRUE )

path<-"~/Documents/IDATS" RGset<-read.metharray.exp(base = path, targets = targets, extended = FALSE,recursive = FALSE, verbose = FALSE, force = FALSE) pData<- pData(RGset) pData$Sample_Name <- as.character(pData$Sample_Name) pData(RGset) <- pData

require(FlowSorted.Blood.450k)

cellCounts <- estimateCellCounts(Reset)

Error in colData(referenceRGset) : no slot of name "colData" for this object of class "RGChannelSet" Error in nrow(x@elementMetadata) : no slot of name "elementMetadata" for this object of class "RGChannelSet"

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[MeganBreitbach]

So you are saying, before I run cellCounts <- estimateCellCounts(RGset)

I should run RGSet<- updateObject(RGset) ??

I tried this, and it did not work.

[kasperdanielhansen]

No, I'm saying that I need to update the reference data stored in the FlowCell.XX package(s) and you can only fix it by updating the package.

On Tue, Dec 6, 2016 at 12:42 PM, Megan notifications@github.com wrote:

So you are saying, before I run cellCounts <- estimateCellCounts(RGset)

I should run RGSet<- updateObject(RGset) ??

I tried this, and it did not work.

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[MeganBreitbach]

I reinstalled the FlowSorted.Blood.450k, minfi, and minfiData, and ran updateObject(FlowSorted.Blood.450k) prior to calling cellCounts <- estimateCellCounts(RGset) and still get the same error

[kasperdanielhansen]

I updated the reference packages a long time ago, so it should have been working for a while. Closing.