fe4960

I tried both the master and dev_geneMismatch versions, the same error in addPeak2GeneLinks with GeneExpressionMatrix persists: "Error in (function (classes, fdef, mtable) : unable to find an inherited method for...

Previously I did not re-run import10xFeatureMatrix() and addGeneExpressionMatrix(), they did not work. This time I installed the dev_geneMismatch branch as below and re-run import10xFeatureMatrix(), addGeneExpressionMatrix(), and addPeak2GeneLinks(). They all work....

Thanks a lot for the reply. Could you let me know the command to show the number of cells in the arrow files? Thanks!

Thanks for the reply! The cell number of each sample in the original ArchR object: ``` > table(proj1@cellColData$Sample) 19_D003_lobe 19_D003_macular 19_D003_macular_NeuN_1 103 152 40 19_D003_macular_NeuN_2 19_D003_macular_NeuN_3 19_D005_lobe 46 56 97...

Thanks for the help. I installed the "dev_idxKeep" branch. It still shows error. > proj2=subsetArchRProject( + ArchRProj = proj1, + cells = final_cell, + outputDirectory = dir, + dropCells =...

I have re-installed dev_idxKeep batch. It shows the error info below. Could you help fix it? Thanks a lot! > proj2=subsetArchRProject( > ArchRProj = proj1, > cells = final_cell, >...

Hi @Jeff1995 , Thanks a lot for the suggestion! I am wondering what is the difference between the parameter "patience" and "reduce_lr_patience" . Indeed, the number of cells significant increased....