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Nanostring-Biostats / GeomxTools

Tools for NanoString GeoMx Digital Spatial Profiler data for reading DCC and PKC files to NanoStringGeomxSet class, Normalization and QC.
MIT License
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mixedModelDE failed to converage #189

Open ydai3 opened 1 year ago

ydai3 commented 1 year ago

Hello, I meet with the following problem when calculating the DEGs between different slides in a GeoMx dataset, Warning messages: 1: In checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, : Model failed to converge with max|grad| = 0.0111628 (tol = 0.002, component 1) 2: Model failed to converge with 1 negative eigenvalue: -4.8e-02

My code is: mixedOutmc <- mixedModelDE(Data_filter[, ind], elt = "log_q", modelFormula = ~ testClass + (1 | SlideName), groupVar = "testClass")

Hope to get ideas on the possible reasons. Will this warning influence the results? If so, how to troubleshoot? Thank you!

maddygriz commented 1 year ago

Hi @ydai3,

Our customer support team will be able to help you with this. Please email support@nanostring.com with your issue.

Thanks, Maddy