I was wondering if anyone could give me advise on calculating the cell counts for cord blood samples in minfi 1.19.
Creating the RGSet including 876 samples works:
> library(minfi) > library(IlluminaHumanMethylation450kanno.ilmn12.hg19) > library(IlluminaHumanMethylation450kmanifest) > RGSet_all<- read.metharray.exp(targets = targets) > validObject(RGSet_all)  TRUE
However, R throws an error when I want to estimate cell counts:
> require(FlowSorted.CordBlood.450k) > counts<-estimateCellCounts(RGSet_final,compositeCellType = "CordBlood", meanplot=TRUE, cellTypes = c("CD8T","CD4T", "NK","Bcell","Mono","Gran","nRBC"),returnAll = FALSE, meanPlot = TRUE, verbose = TRUE, processMethod="preprocessNoob") [estimateCellCounts] Combining user data with reference (flow sorted) data. Error in `[[<-.data.frame`(`*tmp*`, i, value = c("IlluminaHumanMethylation450k", : replacement has 980 rows, data has 876
Any input is welcome. Thanks a lot!