Dont use characters other than letters, numbers, '_' and '.' in the design

[hoelzer]

Note: levels of factors in the design contain characters other than letters, numbers, '' and '.'. It is recommended (but not required) to use only letters, numbers, and delimiters '' or '.', as these are safe characters for column names in R. [This is a message, not a warning or an error]

Although this is not a warning/error, it seems to cause problems in

  coef <- match(
    x = paste(factor, numerator, "vs", denominator, sep = "_"),
    table = resultsNames )

For example, I had the case that coef was NA because of x resulting in condition_6h-IFN_vs_6h-RVFV but in the table I had

> table
[1] "Intercept"                     "condition_6h.IFN_vs_6h.RVFV"
[3] "condition_24h.RVFV_vs_6h.RVFV" "condition_24h.mock_vs_6h.RVFV"
[5] "condition_24h.IFN_vs_6h.RVFV"  "condition_6h.mock_vs_6h.RVFV"

My input files use 24h-RVFV etc... but apparently - is bad.