Question

Uderstanding write.fit output without ID_REF

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moradzadeh_k921 • 0

@moradzadeh_k921-10925

Last seen 8.3 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 • 1.6k views

ADD COMMENT • link 8.5 years ago moradzadeh_k921 • 0

score 1 · Answer 1 · 2016-06-17

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Aaron Lun ★ 28k

@alun

Last seen 3 hours 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.

ADD COMMENT • link 8.5 years ago Aaron Lun ★ 28k

score 0 · Answer 2 · 2016-06-17

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moradzadeh_k921 • 0

@moradzadeh_k921-10925

Last seen 8.3 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?

ADD COMMENT • link 8.5 years ago moradzadeh_k921 • 0

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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.

ADD REPLY • link 8.5 years ago Aaron Lun ★ 28k

score 0 · Answer 3 · 2016-06-17

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moradzadeh_k921 • 0

@moradzadeh_k921-10925

Last seen 8.3 years ago

My problem is resolved.

Thank you very much for your kind answer.

ADD COMMENT • link 8.5 years ago moradzadeh_k921 • 0