differential expression analysis using edgeR

Question

[Liftedkris]

hello experts,

i am using EdgeR for my differential expression analysis. i want to define the contrast of interest but a bug appears with the following error message "unexpected input in "...…." i have gone through my command but i did not detect any typo or any error.

here is my command line

contrasts <- makeContrasts("30hpi" = group30hpi_infected – group30hpi_control, 
                           "90hpi" = group90hpi_infected – group90hpi_control,
                           "180hpi" = group180hpi_infected – group180hpi_control,
                           levels = design)

Error: unexpected input in "contrasts <- makeContrasts("30hpi" = group30hpi_infected –"

please any help to solve this bug would be immensely appreciated

thanks all

[ATpoint]

I reformatted your question a bit to improve readability (code option 10101 in the formatting bar).

An issue could be that the contrast names start with a number. Try naming them as e.g. contr.30hpi, contr.90hpi, contr.180phi or similar.

[Liftedkris]

Thanks for this suggestion but I have tried it but it still doesn’t work

[Benn]

Try to get rid of the double quotes in: "30hpi"=, "90hpi"=, etc., and follow instruction from ATpoint about not starting with a number. See if that works out.

[Liftedkris]

thanks for the response but still does not work. it seems the problem is with the minus sign (-). i have been wondering what went wrong

[h.mon]

In addition to the other suggestions (R really doesn't like variables and columns / row names starting with numbers), it seems to me the probable cause of the error is you are using paragraph marks – instead of minus signs - to define the contrasts. Try:

group30hpi_infected - group30hpi_control

and so on.