Comments (3)
Could you provide the exact code you ran and the error message?
Please make sure you run these two lines to source the functions:
source("https://raw.githubusercontent.com/KlugerLab/ALRA/master/alra.R")
source("https://raw.githubusercontent.com/KlugerLab/ALRA/master/alraSeurat2.R")
Jun
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Hey @JunZhao1990 ,
Thank you for your reply, it's working now!
I do have a question, if I have two samples, 1 control and 1 stimulated, do I merge the two datasets and then do imputation or I do imputation first then merge?
Thank you.
from alra.
@EDYAC, from our experience, it seems that merging and then imputing is best. This also seems to be the experience of these authors, who report ALRA being actually helpful in removing the batch effect when applied to the merged. Their code is here.
If you have other questions regarding multiple samples, please open a separate issue--it helps others find it more easily.
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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
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- Need to deal with R 4.2.0 HOT 5
- Final proportion of non-zero values is large. HOT 2
- Running ALRA with multiple samples HOT 10
- Differential expression HOT 5
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- Which `selection.method` to use for FindingVariableFeatures on ALRA imputed data HOT 2
- 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
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