Question: SingleCellExperiment object cannot be used by Scater package?
0
gravatar for Xingyu
22 months ago by
Xingyu0
Xingyu0 wrote:

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!

ADD COMMENTlink modified 22 months ago by Aaron Lun25k • written 22 months ago by Xingyu0
Answer: SingleCellExperiment object cannot be used by Scater package?
1
gravatar for Aaron Lun
22 months ago by
Aaron Lun25k
Cambridge, United Kingdom
Aaron Lun25k wrote:

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 COMMENTlink modified 22 months ago • written 22 months ago by Aaron Lun25k

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 REPLYlink written 21 months ago by Xingyu0
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