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Fitting failed #86

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xf2297 opened this issue Sep 1, 2023 · 1 comment
Open

Fitting failed #86

xf2297 opened this issue Sep 1, 2023 · 1 comment

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@xf2297
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xf2297 commented Sep 1, 2023

Hi,

I tried to use deMultiplex 2 package for my MULTI-seq data.
However it returns Fitting Failed for my first tag group but works fine for other tags.
Do you guys have any idea why does it happen?
PS: I tried to use another dataset and it works fine too.

rm(list=ls())
data1 <- Read10X('/Users/admin/R/day3raw_feature_bc_matrix')
10X data contains more than one type and is being returned as a list containing matrices of each type.
tag_mtx <- t(data1$Multiplexing Capture)
data(multiseq_oligos)
tag.ref <- multiseq_oligos[3:6]
cell_ids <- Matrix::rowSums(tag_mtx) > 100
tag_used <- Matrix::colSums(tag_mtx) >1e4
tag_mtx <-tag_mtx[cell_ids, tag_used]
res <- demultiplexTags(tag_mtx, plot.path ="./", plot.name = "demux", plot.diagnostics = T)
Running EM for TDBonly
Iteration 1; Q diff: 41543.1943022717
Fitting failed.
Running EM for TDBUrelumab
Iteration 1; Q diff: 41702.5440420353
Iteration 2; Q diff: 3491.6057314845
Iteration 3; Q diff: 4585.20532365606
Iteration 4; Q diff: 493.522236918252
Iteration 5; Q diff: 128.96474546846
Iteration 6; Q diff: 336.784192556333
Iteration 7; Q diff: 91.3320290341871
Iteration 8; Q diff: 32.8050920890091
Iteration 9; Q diff: 0.000563061577850021

@qinzhu
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qinzhu commented Oct 11, 2023

Hi, sorry for the delayed reply. Could you please upload/send me via email (qin.zhu@ucsf.edu) the deMULTIplex2 diagnoistic plot for the "TDBonly" sample? Thanks!

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