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KlugerLab / ALRA

Imputation method for scRNA-seq based on low-rank approximation
MIT License
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alraSeurat2 FUNCTION NOT FOUND!!!! #2

Closed EDYAC closed 5 years ago

EDYAC commented 5 years ago

Hello Everyone, I have installed the rsvd package, when I try to run the alraSeurat2 function, it return an error, saying that the function is not found. Any idea what is going wrong? Thank you.

JunZhao1990 commented 5 years ago

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

EDYAC commented 5 years ago

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.

linqiaozhi commented 5 years ago

@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.