limma list in batchqc_report.html defaults to ComBat corrected version

[joshua-theisen]

When I analyze the bladderdata sample code (below) the limma data are the same in the uncorrected (batchqc_report.html) and the ComBat corrected (combat_batchqc_report.html) reports, and both match the ComBat corrected limma data displayed in the Shiny app, as can be seen in these screenshots (https://drive.google.com/file/d/1kjTFfem_pXqLneKxldAEsfylEtR_v2_b/view?usp=sharing).

Is there a way to fix this?

Thanks Josh

R code used:

pheno <- pData(bladderEset)
edata <- exprs(bladderEset)
batch <- pheno$batch
condition <- pheno$cancer
batchQC(
  edata,
  batch = batch,
  condition = condition,
  report_file = "batchqc_report.html",
  report_dir = ".",
  report_option_binary = "111111111",
  view_report = FALSE,
  interactive = TRUE
)