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MarioniLab / scran

Clone of the Bioconductor repository for the scran package.
https://bioconductor.org/packages/devel/bioc/html/scran.html
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Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘assay’ for signature ‘"dgRMatrix", "character"’ #96

Open houruiyan opened 2 years ago

houruiyan commented 2 years ago

Hello, thank you for your effort to develop this good tools.

I meet some trouble when I use it. My kcadata is a sce data type. image But when I run clusters <- quickCluster(kcadata@assays@data$X) It can run smoothly.

However, when I run computeSumFactors, It has another new question. Hope to get your help. Thank you! image

LTLA commented 2 years ago

For quickCluster, it's expecting an assay called counts. If your count data is differently named, specify it in assay.type.

Same for your first error using computeSumFactors.

For the second error, all compute*Factors functions expect an SCE input. If you have a matrix, use scran::calculateSumFactors instead - see the documentation for more details.