Comments (1)
Wow-apologies for the delay, not sure how this issue escaped us.
I have not tried it on such a large dataset, but ALRA should scale nicely. The time consuming step is the randomized SVD, which is actually very fast. Would be happy to hear if you ended up trying it or not.
As for parameters, ALRA's only parameter is k, which is actually chosen automatically. So I would go with what it chooses, unless you get unfavorable results.
As for using with Seurat, typically you would do the NormalizeData() first.
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Related Issues (20)
- Can I use ALRA imputed matrix to perform the `Find Marker Gene` step ? HOT 2
- Tips for larger matrices? HOT 3
- During FindVariableFeatures after ALRA output, count slot is empty?
- Error in asMethod(object)
- GetAssayData(pbmc, slot = "counts") gives 0 x 0 matrix HOT 1
- Run ALRA in Seurat v4.1.0
- Imputation before other QC steps?
- ALRA and Seurat HOT 1
- Need to deal with R 4.2.0 HOT 5
- alraSeurat2 FUNCTION NOT FOUND!!!! HOT 3
- Final proportion of non-zero values is large. HOT 2
- Running ALRA with multiple samples HOT 10
- Differential expression HOT 5
- Input and Output HOT 3
- Provided normalized function HOT 4
- Imputing integrated data HOT 1
- Input data structure HOT 1
- big data set and K HOT 2
- Input format (genes as rows?) HOT 1
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