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farrellja / URD

URD - Reconstruction of Branching Developmental Trajectories
GNU General Public License v3.0
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Cholmod error #73

Open rojinsafavi opened 3 years ago

rojinsafavi commented 3 years ago

I'm working with a large dataset, and when I try to do PCA I get the following error: axial <- calcPCA(axial, mp.factor = 2)

"2021-06-01 16:30:29: Centering and scaling data."
Error in asMethod(object): Cholmod error 'problem too large' at file ../Core/cholmod_dense.c, line 102
Traceback:

1. calcPCA(axial, mp.factor = 2)
2. getZData(object, genes = genes.use)
3. apply(object@logupx.data[genes, ], 1, mean)
4. as.matrix(X)
5. as.matrix.Matrix(X)
6. as(x, "matrix")
7. asMethod(object)

I am working with the following branch of URD:

devtools::install_github("farrellja/URD@debug")

I manually added the tsne plot . but the same error happens in the next step:

the same thing happens with axial <- calcDM(axial, knn = 100, sigma=16)

jjoung commented 3 years ago

Hi all,

I am also running into the same issues on URD_1.1.1.9000. Did you figure out how to get around it? Looks like the same issue as #56, which has been fixed on URD_1.1.1.9000 for createURD.

@farrellja could you please apply the same fix to calcPCA and calcDM?

Thank you!