Uderstanding write.fit output without ID_REF
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@moradzadeh_k921-10925
Last seen 5.1 years ago

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

 

 

limma • 692 views
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Aaron Lun ★ 27k
@alun
Last seen 1 hour ago
The city by the bay

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.

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@moradzadeh_k921-10925
Last seen 5.1 years ago

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?

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If you want to store your row names in an ID_REF column, you can do:

fit.cont$genes <- data.frame(ID_REF=rownames(fit.cont))

... and then call write.fit as before. You can't do this by specifying row.names because the argument has already been set internally by write.fit when it calls write.table, which leads to the error message that you've observed.

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@moradzadeh_k921-10925
Last seen 5.1 years ago

My problem is resolved.

Thank you very much for your kind answer.

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