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Hi, Thanks for the package. I have applied it a few times successfully, but now I am getting this error.
r/4.3.1 library(FastCAR) library(Matrix) library(Seurat) library(qlcMatrix) library(pheatmap) library(ggplot2) library(gridExtra) library(stringr)
library(FastCAR) library(Matrix) library(Seurat) library(qlcMatrix) library(pheatmap) library(ggplot2) library(gridExtra) library(stringr)
cellMatrix = Read10X("/project/rrg-gturecki/Sarah/Multiplexing_Test/MT_test1/MT_multiseq_INS_PoolE_count_newref/outs/filtered_feature_bc_matrix/") fullMatrix = `Read10X("/project/rrg-gturecki/Sarah/Multiplexing_Test/MT_test1/MT_multiseq_INS_PoolE_count_newref/outs/raw_feature_bc_matrix/") ambProfile = describe.ambient.RNA.sequence(fullMatrix = fullMatrix, start = 50, stop = 500, by = 50, contaminationChanceCutoff = 0.01) pdf(file = "/project/rrg-gturecki/Sarah/Multiplexing_Test/MT_test1/AmbientRNA/MT_INS_PoolE_newref/FastCAR/ambient_profile.pdf", width = 4, height = 4) plot.ambient.profile(ambProfile) dev.off() correctionEffectProfile = describe.correction.effect(fullMatrix, cellMatrix, 50, 500, 50, 0.1) pdf(file = "/project/rrg-gturecki/Sarah/Multiplexing_Test/MT_test1/AmbientRNA/MT_INS_PoolE_newref/FastCAR/correct_effect_heatmap.pdf", width = 4, height = 4) plot.correction.effect.chance(correctionEffectProfile) dev.off() emptyDropletCutoff = recommend.empty.cutoff(ambProfile) emptyDropletCutoff emptyDropletCutoff = 350 contaminationChanceCutoff = 0.05 ambientProfile = determine.background.to.remove(fullMatrix, emptyDropletCutoff, contaminationChanceCutoff) cellMatrix = remove.background(cellMatrix, ambientProfile)
Error in UseMethod("isSymmetric") : no applicable method for 'isSymmetric' applied to an object of class "c('double', 'numeric')"
Thanks!
The text was updated successfully, but these errors were encountered:
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Hi,
Thanks for the package. I have applied it a few times successfully, but now I am getting this error.
r/4.3.1
library(FastCAR) library(Matrix) library(Seurat) library(qlcMatrix) library(pheatmap) library(ggplot2) library(gridExtra) library(stringr)
Error in UseMethod("isSymmetric") :
no applicable method for 'isSymmetric' applied to an object of class "c('double', 'numeric')"
Thanks!
The text was updated successfully, but these errors were encountered: