search

zijianni / SpotClean

R package for decontaminating the spot swapping effect and recovering true expression in spatial transcriptomics data
22 stars 9 forks source link

could spotclean work under situation that all spot 's tissue==1? that my ST data 's tissue position csv 's tissue is all 1,no o,that no backgroud spot #16

Closed hwbdhuidhcoi closed 1 year ago

hwbdhuidhcoi commented 1 year ago

@zijianni

zijianni commented 1 year ago

Hello, in that case SpotClean won't work since it can't tell whether the observed expressions in tissue spots are real or contaminated without the help of background spots.

If your slides were fully covered by tissue, i.e. all spots on the slides are tissue spots, then unfortunately SpotClean can't help. If you are using a filtered data where the background spots have been removed, please go back and use the un-filtered raw data from SpaceRanger output.

hwbdhuidhcoi commented 1 year ago

蟹蟹 @zijianni