Hi Dears,

I have problem with understanding limma results while it doesn't have any column show rawnames(ID_REF). when I use the argument "row.names = TRUE" I get this error:

Error in write.table(tab, file = file, quote = FALSE, row.names = FALSE,  : 
  formal argument "row.names" matched by multiple actual arguments

I will be really grateful if someone help me to resolve my problem. 

Thank you

This has nothing to do with limma, but rather, is because you've specified row.names twice in your write.table call. You say that you set row.names=TRUE, but your error message has row.names=FALSE; it can't be both at the same time.

Thank you for your answer,

The output table of limma, doesn't contain ID_REF column, By using these commands:

>results<- decideTests(fit.cont,lfc = 1)
>write.fit(fit.cont, results, "limma results.txt", adjust="BH",F.adjust = "BH")

and when I add "row.names=TRUE" to previous command (>write.fit(fit.cont, results, "limmaaa.txt", adjust="BH",F.adjust = "BH",row.names=TRUE)), I get this error:

Error in write.table(tab, file = file, quote = FALSE, row.names = FALSE,  : 
  formal argument "row.names" matched by multiple actual arguments

What can i do to represent ID_REF in output table?

My problem is resolved.

Thank you very much for your kind answer.