mixedModelDE gives "object <groupVar> not found" error when replicating vignette.

I am attempting to use the mixedModelDE function for differential expression analysis (post- vs pre-treatment tissue) as per Section 7.3 in the GeoMx Workflows vignette (https://bioconductor.org/packages/release/workflows/vignettes/GeoMxWorkflows/inst/doc/GeomxTools_RNA-NGS_Analysis.html#73_Between_Slide_Analysis:_Diabetic_Kidney_Disease_vs_Healthy). In my case, I am analysing pre- and post-treatment tissue from a single patient, so I have no need to include any variable in the model intercept, but otherwise my code is the same as the vignette. However, mixedModelDE returns "object 'testClass' not found" as an error. This error seems to have been encountered by someone else here: https://bytemeta.vip/repo/Nanostring-Biostats/GeomxTools/issues/174. I have added a "testClass" factor column to my pData and included it in the model formula as in the vignette, so I don't know how to resolve this error.

Here is my code that produces the error: ` pData(target_DSPdata)$testClass <- factor(pData(target_DSPdata)$sample_type)

DEA_results <- c() for(segmt in DSP_segs){ ind <- pData(target_DSPdata)$segment == segmt mixedOutmc <- mixedModelDE(target_DSPdata[, ind], elt = "log2_Q3_norm", modelFormula = ~ testClass + 1, groupVar = "testClass", nCores = 1, #parallel::detectCores(), multiCore = FALSE)

r_test <- do.call(rbind, mixedOutmc["lsmeans", ]) tests <- rownames(r_test) r_test <- as.data.frame(r_test) r_test$Contrast <- tests

r_test$Gene <- unlist(lapply(colnames(mixedOutmc), rep, nrow(mixedOutmc["lsmeans", ][[1]]))) r_test$Subset <- segmt r_test$FDR <- p.adjust(r_test$Pr(>|t|), method = "fdr") r_test <- r_test[, c("Gene", "Subset", "Contrast", "Estimate", "Pr(>|t|)", "FDR")] DEA_results <- rbind(DEA_results, r_test) } `

This returns the following error:

Error in eval(predvars, data, env) : object 'testClass' not found

Nanostring-Biostats / GeomxTools

mixedModelDE gives "object <groupVar> not found" error when replicating vignette. #187