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. Loading required package: IlluminaHumanMethylation450kanno Error in getAnnotationObject(object) : cannot load annotation package IlluminaHumanMethylation450kanno In addition: Warning message: 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.