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Vivianstats / scImpute

Accurate and robust imputation of scRNA-seq data
https://www.nature.com/articles/s41467-018-03405-7
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Imputation error #34

Open kin182 opened 3 years ago

kin182 commented 3 years ago

Hi Vivian,

Thank you so much for the scImpute package. I am relatively new to it and I am still learning.

When I ran with the code below with v0.0.9

scimpute("test.csv"), infile="csv", outfile="csv", out_dir="data/", labeled=TRUE, labels=as.vector(cluster_labels),
    type="TPM", genelen=genelength, drop_thre=0.5, ncores=5)

I got through the following with errors

[1] "reading in raw count matrix ..."
[1] "number of genes in raw count matrix 12371"
[1] "number of cells in raw count matrix 15230"
[1] "reading finished!"
[1] "imputation starts ..."
[1] "searching candidate neighbors ... "
[1] "calculating cell distances ..."
starting worker pid=32606 on localhost:11462 at 19:33:49.328
[1] "estimating dropout probability for type 1 ..."
[1] 2000
[1] 4000
[1] 6000
[1] 8000
[1] 10000
[1] 12000
[1] "searching for valid genes ..."
[1] "imputing dropout values for type 1 ..."
Loading required package: scImpute
Loading required package: parallel
Loading required package: penalized
Loading required package: survival
Welcome to penalized. For extended examples, see vignette("penalized").
Loading required package: doParallel
Loading required package: foreach
Loading required package: iterators
loaded scImpute and set parent environment
Error in qr.coef(qr(a, LAPACK = TRUE), b) : 
    error code 5 from Lapack routine 'dtrtrs'
Error in qr.coef(qr(a, LAPACK = TRUE), b) : 
    error code 11 from Lapack routine 'dtrtrs'
Error in qr.coef(qr(a, LAPACK = TRUE), b) : 
    error code 5 from Lapack routine 'dtrtrs'
Error in qr.coef(qr(a, LAPACK = TRUE), b) : 
    error code 6 from Lapack routine 'dtrtrs'
....
[1] 100
Error in qr.coef(qr(a, LAPACK = TRUE), b) : 
    error code 8 from Lapack routine 'dtrtrs'
Error in qr.coef(qr(a, LAPACK = TRUE), b) : 
    error code 5 from Lapack routine 'dtrtrs'
Error in qr.coef(qr(a, LAPACK = TRUE), b) : 
    error code 9 from Lapack routine 'dtrtrs'

I have not been able to figure out what happened. Any help would be appreciated! Thank you.

ice4prince commented 3 years ago

I have the same issue with you!

ice4prince commented 3 years ago

Have you found out why?

kin182 commented 3 years ago

I think it is something related to the TPM or the genelength file. See if it still happens when you use count matrices, which is the recommended input file, if possible.

rrchai commented 1 year ago

any updates on this issue?