PrepareSpatialDecon error message

[emiliasiukola]

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]

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.