I have successfully run_scINSIGHT and got the real.scobj object, following the tutorial you gave.
It chooses k=7.
When I run the following code I get an error:
da_tsne = data.frame(tSNE1 = res_tsne$Y[,1], tSNE2 = res_tsne$Y[,2], sample = sample, condition = condition, celltype = celltype, clusters = clusters)
# Error in data.frame(tSNE1 = res_tsne$Y[, 1], tSNE2 = res_tsne$Y[, 2], :
# Parameter values mean different row numbers: 105433, 105434
This looks like there is an inconsistency in the length of the parameters. So I checked the individual inputs:
I found that cluster has one more element than other input.
clusters = as.character(unlist(real.scobj@clusters))
but sample,condition,celltype are from real.counts.
So I checked real.counts and real.scobj and found that real.scobj has one more element than real.counts, I don't know why
real.counts:
real.scobj:
Could you please tell me which step I might have gone wrong, thank you very much!
I have successfully run_scINSIGHT and got the real.scobj object, following the tutorial you gave.
It chooses k=7. When I run the following code I get an error:
da_tsne = data.frame(tSNE1 = res_tsne$Y[,1], tSNE2 = res_tsne$Y[,2], sample = sample, condition = condition, celltype = celltype, clusters = clusters)This looks like there is an inconsistency in the length of the parameters. So I checked the individual inputs:
I found that cluster has one more element than other input.
clusters = as.character(unlist(real.scobj@clusters))but sample,condition,celltype are from real.counts.So I checked real.counts and real.scobj and found that real.scobj has one more element than real.counts, I don't know why real.counts:
real.scobj:
Could you please tell me which step I might have gone wrong, thank you very much!