Liqa, DAS: Error in optim(start, fn.opt, method = method, control = control) : non-finite value supplied by optim

[sigusn]

Hi

I´m running the demo data you supply. with this command line
liqa -task diff -condition_1 list1 -condition_2 list2 -out das_detection_results
I get the following output
DAS testing: Gene ATP5PF being processed...Error in optim(start, fn.opt, method = method, control = control) :
initial value in 'vmmin' is not finite
DAS testing: Gene IL10RB being processed...Error in optim(start, fn.opt, method = method, control = control) :
non-finite value supplied by optim
DAS testing: Gene S100B being processed...Done!
DAS testing: Gene OLIG1 being processed...Done!
DAS testing: Gene SOD1 being processed...Done!
DAS testing: Gene IFNAR1 being processed...Done!
DAS testing: Gene DSCAM-AS1 being processed...Done!
DAS testing: Gene GABPA being processed...Done!

When opening the das_detection_results file the two genes with error are missing. Same thing happens when I´m running our own data.
What does this "error in optim" mean and what can be done to resolve it?

[huyustats]

Hi,

Basically to generate more reliable detection results, optim function removes genes with expressions that failed in fitting the beta regression model. Let me check the quantification output. Thanks

[sigusn]

Thanks, this is just from the demo data I downloaded. So in the isoform_expression_summary all the genes have some values, but the ATP5PF and IL10RB are missing from the das detection due to this error.