edroaldo

You have to do either: cellrouter data > cellrouter + min.genes=0) > [1] "Initializing CellRouter object" > > > metadata > cellrouter > > cellrouter Show Traceback > > Rerun...

Can you please try like this: cellrouter > > > > > cellrouter > cellrouter [1] "building k-nearest neighbors graph" > Show Traceback > > Rerun with Debug > Error...

Also, were you able to reproduce the tutorial with no errors? I am just checking if that could be some package missing on your side... thanks! 2018-07-31 10:08 GMT-04:00 Edroaldo...

No problem. Can you please check if you have the following packages: library('cccd') library('proxy') I think this might be missing in your R installation. You can install this using: source('https://bioconductor.org/biocLite.R')...

Did you run the entire cellrouter workflow? Did you perform the PCA analysis with: cellrouter Thank you, > > Likely I have both already installed > > > library('cccd') >...

You need to run the entire workflow. Are you running the tutorial line by line? It is very weird to have an error in as.dist(matrix) unless "matrix" is empty. Also,...

This looks fine... but an error in plotReducedDimension is very strange... it basically plots the output of computeTSNE... Can you send me the info I asked for in the previous...

Everything look just fine... very strange... You can try this to save in your local folder: plotReducedDimension(cellrouter, reduction.type = 'tsne', dims.use = c(1,2), annotation = "celltype", annotation.color = 'celltype_color', showlabels...

You seem to be mixing the tutorial with outr data without update information. If you are using your data, you should do: plotReducedDimension(cellrouter, reduction.type = 'tsne', dims.use = c(1,2), annotation...

You do not have " annotation = "celltype" " in your analysis, this is specific to the tutorial, where "celltype" was previously defined at the beginning of the analysis. 2018-07-31...