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DavisLaboratory / standR

Spatial transcriptomics analyses and decoding in R
https://davislaboratory.github.io/standR/
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PrepareSpatialDecon error message #33

Open emiliasiukola opened 2 months ago

emiliasiukola commented 2 months ago

When using the code: spd <- prepareSpatialDecon(spe_tmm)

we are getting error message: "NegProbe-WTXmust be included in the dataset. Perhaps specify rmNegProbe=TRUE when using readGeoMx" when using prepareSpatialDecon. We are using WTA so there are several negative probes, however we do not understand what the pool= variable in the command should look like. We have already specified rmNegProbe=TRUE when using readGeoMx.

Regards, Emilia

ningbioinfo commented 2 months ago

Hi @emiliasiukola , the input for the pool argument is a vector with length of the genes, i.e. nrow(spe). It should be something like c("negprob1","negprob1","negprob1","negprob2","negprob2","negprob2"..., "negprobx"), so it tells the function with negative probes is governing which genes.