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immunogenomics / harmony

Fast, sensitive and accurate integration of single-cell data with Harmony
https://portals.broadinstitute.org/harmony/
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Error: matrix multiplication: incompatible matrix dimensions: 100x96490 and 96489x22 #237

Open claireanjou opened 7 months ago

claireanjou commented 7 months ago

When I am running RunHarmony, it produces this error message. What could this mean? I have ran the same code before and never encountered this error. Would appreciate any help, thanks!

ERROR MESSAGE: Error: matrix multiplication: incompatible matrix dimensions: 100x96490 and 96489x22 In addition: Warning messages: 1: In theta (1 - exp(-(N_b/(nclust tau))^2)) : longer object length is not a multiple of shorter object length 2: In rbind(rep(1, N), phi) : number of columns of result is not a multiple of vector length (arg 1)

CODE SAMPLE: pbmc_small <- FilterGenes(object = pbmc_small, min.value = 0.5, min.cells = 100) pbmc_small <- NormalizeData(pbmc_small) pbmc_small <- FindVariableFeatures(pbmc_small, selection.method = "vst", nfeatures = 2000) pbmc_small <- ScaleData(pbmc_small, features = rownames(pbmc_small))

pbmc_small <- RunPCA(pbmc_small, features = VariableFeatures(object = pbmc_small))

pbmc_small@meta.data$library_id <- as.factor(pbmc_small@meta.data$library_id)

pbmc_small <- RunHarmony(pbmc_small, group.by.vars="library_id", verbose = TRUE)

pati-ni commented 6 months ago

Hi @claireanjou,

sorry for the delayed response. Can you share your sessionInfo() to determine your Seurat and harmony versions?