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DavisLaboratory / standR

Spatial transcriptomics analyses and decoding in R
https://davislaboratory.github.io/standR/
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spatialdecon #24

Closed OnkarMulay closed 5 months ago

OnkarMulay commented 8 months ago

Hi @ningbioinfo ,

Thanks for the tool.

If there are multiple negative probes then bg <- as.data.frame(norm*0) -> this change needs to be made in the original function.

I'm getting this error on running spatialdecon though Error in solve.default(fit$hessian): Lapack routine dgesv: system is exactly singular: U[1,1] = 0

Code:

res <- spatialdecon(norm = spd$normCount,
                               bg = spd$backGround,
                               X = safeTME,
                               cellmerges = safeTME.matches,
                               resid_thresh = 1,lower_thresh = 0.1)

Please let me know how can I solve this issue. Thanks

ningbioinfo commented 8 months ago

Hi @OnkarMulay , if you have multiple negative probes, can you try the negProbeName and pool parameters from the prepareSpatialDecon function?