limmaFit error when comparing TCGA RNA-Seq data

Question

[vernonlim98]

I am trying to compare TCGA RNA-Seq data between platinum-sensitive and platinum-resistant samples.

I reference the workflow posted here: https://cran.r-project.org/web/packages/easybio/vignettes/example_limma.html

I have gotten so far:

query_ov = GDCquery(project = "TCGA-OV", 
                data.category = "Transcriptome Profiling",
                experimental.strategy = "RNA-Seq",
                access = "open",
                sample.type = c("Primary Tumor", "Solid Tissue Normal"))
data = GDCprepare(query = query_ov, summarizedExperiment = TRUE)
lt = prepare_tcga(data)    
pfi_tcga = read_excel("2010-09-11380C-Table_S1.2.xlsx") #this is to retrieve the clinical data from TCGA, and to label the samples as platinum-resistant/sensitive
lt$all$sampleInfo = left_join(lt$all$sampleInfo, pfi_tcga, by = c("patient" = "BCRPATIENTBARCODE"))
lt$all$sampleInfo = lt$all$sampleInfo|>
  filter(PlatinumStatus == "Resistant" | PlatinumStatus == "Sensitive")

lt$all$exprCount = lt$all$exprCount[,lt$all$sampleInfo$barcode]

rownames(lt$all$sampleInfo) = lt$all$sampleInfo$barcode

x = dgeList(lt$all$exprCount, lt$all$sampleInfo, lt$all$featuesInfo)
x = dprocess_dgeList(x, "PlatinumStatus", 10)
efit = limmaFit(x, "PlatinumStatus")
x$samples$PlatinumStatus = relevel(as.factor(x$samples$PlatinumStatus), ref= "Sensitive")

When I try to limmaFit, I get the following error:

Error in limma::makeContrasts() : 
  argument "levels" is missing, with no default

Does anyone know what is the error referring to? I am not using any makeContrasts, and the error still shows up even though I have established levels in PlatinumStatus

[ATpoint]

Seriously, an ordinary limma-voom analysis between two groups is as little of 5 lines of code. Please read the limma user guide which covers this. These wrapper packages are blackboxes, you do not know (unless inspecting source code) if they're applying the current best practices as by the limma authors.