Imputation error

[kin182]

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]

I have the same issue with you!

[ice4prince]

Have you found out why?

[kin182]

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]

any updates on this issue?