Question

SingleCellExperiment object cannot be used by Scater package?

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Xingyu • 0

@xingyu-15031

Last seen 6.5 years ago

Hi,

I'm learning how to do simple analysis to single cell sequencing data from this workflow http://bioconductor.org/help/workflows/simpleSingleCell/#denoising-expression-values-using-pca#cmid=172561

In the QC step, it used the function calculateQCMetrics. But I got warning: Error in calculateQCMetrics(sce, feature_controls = list(ERCC = is.spike, : object must be an SCESet object.

sce is defined as SingleCellExperiment object because it will use colData() function of SingleCellExperiment in the following step. Thus, there seems no way to change sce from SingCellExperiment to SCESet object. I know this is not a problem in the older version of Scater package, so SingleCellExperiment object cannot be used by Scater package now?

Thanks!

scater singlecellexperiment simplesinglecell • 2.0k views

ADD COMMENT • link updated 6.8 years ago by Aaron Lun ★ 28k • written 6.8 years ago by Xingyu • 0

score 1 · Accepted Answer · 2018-02-15

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Aaron Lun ★ 28k

@alun

Last seen 12 hours ago

The city by the bay

I'm not sure I understand how you managed to get this error message. Are you using the latest version of scater (1.6.3)? The only error message in the current release version of the calculateQCMetrics function is "object must be a SingleCellExperiment". I assume you are using an older version of the package; posting your session information is usually recommended when asking questions.

ADD COMMENT • link 6.8 years ago Aaron Lun ★ 28k

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Hi Aaron,

Thanks for your answer. Yes, I checked it and found it was an old version because I used the old version of Bioconductor. After I updated it and reinstall the latest version of scater, it works well! Thanks so much!

ADD REPLY • link 6.8 years ago Xingyu • 0