DESeq error on differential report

[arugula2388]

Any suggestions on what is a causing this error. I loaded the data using loadDsAcc within a prior analysis/data/ ds_ATAC_filtered and or Processed

createReport_differential(dsa, reportDir) Last executed at 2023-05-24 14:18:51 in 20.65s 2023-05-24 14:18:31 12.4 WARNING An extensive amount of comparisons will be performed. Consider being more specific in the differentialColumns and differentialCompNames options. 2023-05-24 14:18:31 12.4 STATUS STARTED Computing differential accessibility 2023-05-24 14:18:31 12.4 STATUS STARTED Differential accessibility objects 2023-05-24 14:18:31 12.4 STATUS Region type: tiling500bp converting counts to integer mode

Warning message in DESeqDataSet(se, design = design, ignoreRank): “some variables in design formula are characters, converting to factors” the design formula contains one or more numeric variables with integer values, specifying a model with increasing fold change for higher values. did you mean for this to be a factor? if so, first convert this variable to a factor using the factor() function

the design formula contains one or more numeric variables that have mean or standard deviation larger than 5 (an arbitrary threshold to trigger this message). Including numeric variables with large mean can induce collinearity with the intercept. Users should center and scale numeric variables in the design to improve GLM convergence.

Error in checkFullRank(modelMatrix): the model matrix is not full rank, so the model cannot be fit as specified. One or more variables or interaction terms in the design formula are linear combinations of the others and must be removed.

Please read the vignette section 'Model matrix not full rank':

vignette('DESeq2') Traceback:

1. createReport_differential(dsa, reportDir)
2. createReport_differential(dsa, reportDir)
3. .local(.object, ...)
4. lapply(regionTypes, FUN = function(rt) { . logger.status(c("Region type:", rt)) . do <- getDESeq2Dataset(.object, rt, adjCols, compTab = compTab) . fn <- file.path(rDir.data.abs, paste0("diffObj_", normalize.str(rt, . return.camel = TRUE), ".rds")) . saveRDS(do, fn) . return(do) . })
5. FUN(X[[i]], ...)
6. getDESeq2Dataset(.object, rt, adjCols, compTab = compTab)
7. getDESeq2Dataset(.object, rt, adjCols, compTab = compTab)
8. .local(.object, ...)
9. DESeq2::DESeqDataSetFromMatrix(countData = cm, colData = ph, . design = designF)
10. DESeqDataSet(se, design = design, ignoreRank)
11. checkFullRank(modelMatrix)
12. stop("the model matrix is not full rank, so the model cannot be fit as specified.\n One or more variables or interaction terms in the design formula are linear\n combinations of the others and must be removed.\n\n Please read the vignette section 'Model matrix not full r