issue running tutorial

[mkunst23]

Hi.

I'm trying to run the tutorial on the striatum dataset but when I try to infer gene expression I get this error message:

NA_merFISH_iSpatial = iSpatial::infer(NA_merFISH, NA_scRNA)
1st level integration
|++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=04s
normalization
2nd level integration
Error in harmonyObj$cluster_cpp() :
element-wise pow(): incompatible matrix dimensions: 100x2 and 2x1

Michael

[Czh3]

Hi Michael,

It seems harmony did not be install successfully. Please see: immunogenomics/harmony#171

Can you run the harmony tutorial? https://github.com/immunogenomics/harmony

Chao

[mkunst23]

Hi Chao,

I have been trying but ran into some problems (similar to the ones described in the issues). I'll keep you posted.

Michael

[mkunst23]

I fixed it by running

devtools::install_github("eddelbuettel/harmony",force = TRUE)

But now I get this problem

NA_merFISH_infer = infer_v2(NA_merFISH, NA_scRNA)
1st level integration
|++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=05s
2nd level integration
Error in irlba(A = t(x = object), nv = npcs, ...) :
max(nu, nv) must be positive

[Czh3]

The NA_scRNA object has 26145 genes across 6000 cells, and NA_merFISH has 253 genes across 6000 cells.

Make sure the example data are intact.