MAESTRO
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liulab-dfci
ATACRunSeurat..RunSVD->RunSVD.Assay->RunSVD.default->irlba
When I run MAESTRO on the ATACseq tutorial (atac_pbmc_500_nextgem), I get the above error. If I probe further, the error is: Error in irlba(A = t(x = object), nv = n, work = irlba.work) : max(nu, nv) must be positive Is there something wrong with the dataset? Did something else change, recently? I tested and this does not have to do with #123. The error still occurs after fixing that.
Context: Chromap built by hand due to current errors preventing it from running when installed via other mechanisms. Otherwise, the rest of the environment installed through conda. The MASESTRO version is 1.5.1
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Hi, sorry for the late response! I have test the ATACseq pipeline following the tutorial with the atac_pbmc_500_nextgem_filtered_peak_bc_matrix.h5 file as input. MAESTRO V1.5.1 seems to work for me. Here I attach the codes for your reference.
library(MAESTRO)
library(Seurat)
pbmc.peak <- Read10X_h5("atac_pbmc_500_nextgem_filtered_peak_bc_matrix.h5")
pbmc.gene <- ATACCalculateGenescore(pbmc.peak, organism = "GRCh38")
pbmc.ATAC.res <- ATACRunSeurat(inputMat = pbmc.peak,
project = "atac_pbmc_500_nextgem",
min.c = 50,
min.p = 500,
method = "LSI",
dims.use = 1:30,
cluster.res = 0.6,
only.pos = TRUE,
peaks.test.use = "presto",
peaks.cutoff = 1e-05,
peaks.pct = 0.1,
peaks.logfc = 0.2,
outdir = ".")
