de_analysis, group_col names

[DavidGO464]

Hi!,

having this in the documentation: "de_analysis(data, ..., measure = "Area", group_col = NULL)"

I created a lipidomics experiment and then added the annotation ("d1"). The data set of the annotation has two columns (the first is "Sample" and the second is "fibrosis_score_adj", this score are numerical ranges like 0-2 vs 3-4) when I set the name of the column in the "group_col" argument:

de_analysis(d1, 0-2 - 3-4, measure = "Area", group_col = fibrosis_score_adj)

the output is:

Error in de_analysis(d, 0 - 2 - 3 - 4, measure = "Area", group_col = "fibrosis_score_adj") : No contrasts provided

How can I make de_analysis work properly?

and also, what do you recommend to put first in the "..." argument of de_analysis: the control or the experimental?

kind regards

by the way: Yes, the categories inside "fibrosis_score_adj" are "0-2" and "3-4"

[ahmohamed]

Your annotation column is treated numeric continuous variable. If we want it categorical, you can convert it to character. To be safe, just add any prefix to your scores. Something like d1$fibrosis_score_adj = paste0("FS", d1$fibrosis_score_adj) would work. And your de_analysis would become de_analysis(d1, (FS0-FS2) - (FS3-FS4), measure = "Area", group_col = fibrosis_score_adj)

[ahmohamed]

Sorry just noticed your last line. Ignore the comment above.

The safe way is to syntactically valid variable names in R. For example R0_2 (no spaces, minus, doesn't start with a number). Alternatively you can try to enclose your variables with back ticks like that:

de_analysis(d1, `0-2` - `3-4`, measure = "Area", group_col = "fibrosis_score_adj")

Note also the group_col needs double qoutes.

[DavidGO464]

Thank you so much!!!