Hi (I think @ningbioinfo ),
I've been attempting to run Spatial Decon for WTA data, which has multiple negative probes. (I've read the discussions / issues here regarding them, but am still at loss).
Here's the code up to spatial decon:
spe2 <- readGeoMx(countFile2, sampleAnnoFile, featureAnnoFile2, rmNegProbe = F)
spe2 <- addPerROIQC(spe2, rm_genes = TRUE)
qc <- colData(spe2)$AOINucleiCount > 100
spe2 <- findNCGs(spe2, batch_name = "SlideName", top_n = 300)
spe_ruv2 <- geomxBatchCorrection(spe2, factors = "SegmentLabel",
NCGs = metadata(spe)$NCGs, k = 4)
I have 139 negative probes, named NegProbe-WTX_1, NegProbe-WTX_2, NegProbe-WTX_3 and so on. The names are unique.
When I attempt to run prepareSpatialDecon, I get an error saying that NegProbe-WTX must be included in the dataset. If I understand correctly, it would require exact name match, "NegProbe_WTX", which I do not have - admittedly, it does work if I instead but "NegProbe-WTX1", but I doubt that's the correct play here.
##So this works, in theory
spd=prepareSpatialDecon(spe_ruv2, negProbeName = "NegProbe-WTX_1",
pool = nrow(spe_ruv2))
So how do I run prepareSpatialDecon so that it handles multiple negative probes?
Secondly, regarding the same function; I understand argument "pool" requires a number. Is that number supposed to be number of negative probes in the dataset, number of genes or number of negative probes + genes (aka number of rows). I did test with all the values, and resulting data frames are exact matches, through.
Hi (I think @ningbioinfo ),
I've been attempting to run Spatial Decon for WTA data, which has multiple negative probes. (I've read the discussions / issues here regarding them, but am still at loss).
Here's the code up to spatial decon:
I have 139 negative probes, named NegProbe-WTX_1, NegProbe-WTX_2, NegProbe-WTX_3 and so on. The names are unique.
When I attempt to run prepareSpatialDecon, I get an error saying that NegProbe-WTX must be included in the dataset. If I understand correctly, it would require exact name match, "NegProbe_WTX", which I do not have - admittedly, it does work if I instead but "NegProbe-WTX1", but I doubt that's the correct play here.
So how do I run prepareSpatialDecon so that it handles multiple negative probes?
Secondly, regarding the same function; I understand argument "pool" requires a number. Is that number supposed to be number of negative probes in the dataset, number of genes or number of negative probes + genes (aka number of rows). I did test with all the values, and resulting data frames are exact matches, through.