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Question: minfi - estimatecellcount function
0
2.9 years ago by
AST50
INDIA
AST50 wrote:

Recently, I am facing a problem while estimating the cell count and also while using Quantile preprocessing in minfi v1.14.0 (R v3.2.2). I have visited the epigenomic forum but found no answer to that.

> estimateCellCounts(rgSet450k, compositeCellType="Blood",cellTypes=c("CD8T","CD4T", "NK","Bcell","Mono","Gran"), returnAll=TRUE, meanPlot=FALSE, verbose=TRUE)
Loading required package: FlowSorted.Blood.450k [estimateCellCounts] Combining user data with reference (flow sorted) data.
Error in combine(rgSet, referenceRGset) :   objects have different annotations: IlluminaHumanMethylation450k, IlluminaHumanMethylation450kilmn12.hg19

Here the problem is there is no such package available at Bioconductor as 'IlluminaHumanMethylation450kanno'. Currently available annotation file is "IlluminaHumanMethylation450kanno.ilmn12.hg19".

> preprocessQuantile(rgSet450k, fixOutliers = TRUE, removeBadSamples = TRUE, badSampleCutoff = 10.5, quantileNormalize = TRUE, stratified = TRUE, mergeManifest = FALSE, sex = NULL, verbose = TRUE)
[preprocessQuantile] Mapping to genome.
Error in getAnnotationObject(object) :
In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :  there is no package called ‘IlluminaHumanMethylation450kanno’

Can you please suggest a possible way through.
Thanks

modified 2.9 years ago by Kasper Daniel Hansen6.4k • written 2.9 years ago by AST50
1
2.9 years ago by
United States
Kasper Daniel Hansen6.4k wrote:
Your rgset450k is very old. You can fix this either by 1) recreate your rgset450k object 2) do rgset450k = updateObject(rgset450k) 3) (a bit dangeorus) rgset450k@annotation = RGsetEx@annotation (where RGsetEx comes from minfiData). Option (2) is the recommended one, and I am pretty sure it should fix it, but I could be remembering it wrongly; its a long time since this change happened. Kasper

I have the same problem. Evrything worked fine until yesterday and today I get the following error message when I try to use preprocessFunnorm function in minfi (see below in bold). I have tried the first 2 fixes you suggested (no luck!). Are you able to think of anything else?

Regards,

Poojitha

rgSet_blood_funnorm<-preprocessFunnorm(rgSet_blood)
[preprocessFunnorm] Background and dye bias correction with noob
Error in getAnnotationObject(object) :
In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
there is no package called ‘IlluminaHumanMethylation450kanno’