Hi,
I was trying to use minfi to estimate cell counts, but get an error. I can't make out what I need to change in the sample sheet. Here is my code with the error:
> RGsetx <- read.450k.exp(targets = ssminfi)
>
> beta <- getBeta(RGsetx)
> phenoData <- pData(RGsetx)
>
> cellCountsASD <- estimateCellCounts(RGsetx)
[estimateCellCounts] Combining user data with reference (flow sorted) data.
Error in combine(pDataX, pDataY) : data.frames contain conflicting data:
non-conforming colname(s): Array, Basename
> traceback()
9: stop("data.frames contain conflicting data:", "\n\tnon-conforming colname(s): ",
paste(sharedCols[!ok], collapse = ", "))
8: combine(pDataX, pDataY)
7: combine(pDataX, pDataY)
6: .local(x, y, ...)
5: combine(phenoData(x), phenoData(y))
4: combine(phenoData(x), phenoData(y))
3: combine(rgSet, referenceRGset)
2: combine(rgSet, referenceRGset)
1: estimateCellCounts(RGsetx)
> head(phenoData,2)
Sample_Name Sample_Well Sample_Plate Sample_Group Pool_ID Array Slide
5775446050_R01C02 5775446050_R01C02 B01 1 UNKNOWN GS0007001-OMA R01C02 5775446050
5775446050_R04C02 5775446050_R04C02 B04 1 UNKNOWN GS0007001-OMA R04C02 5775446050
Basename
5775446050_R01C02 /Volumes/ext/idat/5775446050/5775446050_R01C02
5775446050_R04C02 /Volumes/ext/idat/5775446050/5775446050_R04C02
filenames
5775446050_R01C02 /Volumes/ext/idat/5775446050/5775446050_R01C02
5775446050_R04C02 /Volumes/ext/idat/5775446050/5775446050_R04C02
> colnames(beta)[1:5]
[1] "5775446050_R01C02" "5775446050_R04C02" "5775446050_R04C01" "5775446050_R05C02" "5775446050_R03C02"
thanks for any help!
