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hansenlab / minfi

Devel repository for minfi
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estimateCellCounts() error (extended RGset file and EPIC array) #120

Open ghost opened 6 years ago

ghost commented 6 years ago

Hello We tried estimateCellCounts() with an extended RGChannelset data from EPIC array. We got this.

counts <- estimateCellCounts(dat) Loading required package: FlowSorted.Blood.450k Loading required package: IlluminaHumanMethylation450kmanifest Loading required package: IlluminaHumanMethylationEPICmanifest [estimateCellCounts] Combining user data with reference (flow sorted) data.

[estimateCellCounts] Processing user and reference data together.

[preprocessQuantile] Mapping to genome. Loading required package: IlluminaHumanMethylation450kanno.ilmn12.hg19 Error in validObject(.Object) : invalid class “RangedSummarizedExperiment” object: undefined class for slot "rowRanges" ("GenomicRangesORGRangesList") Calls: estimateCellCounts ... .new_RangedSummarizedExperiment -> new -> initialize -> initialize -> validObject Execution halted

Can anyone help us? Thank you in advance. AB

kasperdanielhansen commented 6 years ago

What version of minfi? What is the output of validObject(dat); if it was created with an "old" version of minfi you may have to run updateObject() on it.

ghost commented 6 years ago

validObject(dat) [1] TRUE Still the same error... any other suggestion? Thank you so much!

ghost commented 6 years ago

I have R 3.4.0 and minfi 1.23.3. I am trying to find out whether it is related to old VariantAnnotation package. I am having hard time upgrading VariantAnnotation. I will let you know if it works.

ghost commented 6 years ago

Worked after installing R & packages on a local folder.