Works for me using minfi 1.19.14 and the RGsetEx from minfiData. Need more information. Kasper On Fri, Sep 23, 2016 at 5:05 PM, darina [bioc] <noreply@bioconductor.org> wrote: > Activity on a post you are following on support.bioconductor.org > > User darina <https: support.bioconductor.org="" u="" 11539=""/> wrote Question: > estimate cell counts in CordBlood using mini > <https: support.bioconductor.org="" p="" 87434=""/>: > > Dear all, > > 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) > > [1] 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! > > > > Darina > > ------------------------------ > > Post tags: minfi, cellcounts, cordblood > > You may reply via email or visit estimate cell counts in CordBlood using mini >