estimate cell counts in CordBlood using mini
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darina • 0
@darina-11539
Last seen 6.4 years ago

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

minfi cellcounts cordblood • 967 views
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@kasper-daniel-hansen-2979
Last seen 4 months ago
United States
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 >
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Entering edit mode
darina • 0
@darina-11539
Last seen 6.4 years ago

Thanks Kasper,

I updated minfi to 1.19.14 and also Biobase to 2.33 and now it works.

Best,

Darina 

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