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dbdimitrov / BingleSeq

BingleSeq - A user-friendly R package for Bulk and Single-cell RNA-Seq data analyses
MIT License
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metadata for 10x single cell data? #8

Closed nicinkjh closed 2 years ago

nicinkjh commented 3 years ago

I have two questions. 1) Is it possible to load metadata for single cell RNAseq in BingleSeq?

2) I have 10x count data of 49 cells which are fewer than 50. It creates issue when running unsupervised clustering, because default setting is 50 cells. But I cannot change in BingleSeq module.

Warning: Error in irlba: max(nu, nv) must be strictly less than min(nrow(A), ncol(A))

Do you have suggestion?

Thanks,

dbdimitrov commented 3 years ago

Hi,

I can double check it try to have it solved by end of next week.

Thanks for opening an issue :)

dbdimitrov commented 3 years ago

Hi again,

You are right, I think the issue likely arises from the PCA dimensionality reduction which is by default set to 50 PCs. However, I'm not sure if setting it to a lower value on my side would be the best solution either, as I prefer to keep the tool as generalize as possible, and I think the comparatively low dimensionality of your dataset is a bit specific.

One solution could be to fork the repo and change the following line on your side: scaled_object <- RunPCA(scaled_object, features = VariableFeatures(object = scaled_object)) to e.g. scaled_object <- RunPCA(scaled_object, features = VariableFeatures(object = scaled_object), npcs=30)

Also, at this stage, BingleSeq does not support external metadata for scRNA-Seq.

Thanks!