This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Removing Duplicate Rows(Gene Names)

Hi,

How can I remove duplicate rows from the output of my toptableF? I have tried the following without success:

  if (unique(fit2$genes)){
  Sigenes.F <- topTableF(fit2, number=100, genelist=fit2$genes, adjust.method="bonferroni",
                   sort.by="F")
  }

Thanks

microarray r
• 11,246 views • link
updated by Michael Dondrup Michael Dondrup • written by robjohn7000 robjohn7000

Is it from the fit2 data frame or the Sigenes.F data frame that you want to remove the duplicates?

• 0 views • link
written by Joseph Hughes Joseph Hughes

From the Sigenes.F data frame. Thanks.

• 0 views • link
written by robjohn7000 robjohn7000

you can do as Michael Dondrup says below, but that might be removing important information. Often, you have duplicated genes in microarray data because there are multiple probes for a single gene. E.g. what if one of them is up-regulated and one is down-regulated (due to alternative transcript use) and you discard one?

• 335 views • link
written by brentp brentp

I don't think you want to remove duplicated genes, you probably want to keep the best p-value for each gene. Have a look into the aggregate() function

• 81 views • link
written by Irsan Irsan

Thanks again, Irsan. I was able to get get aggregate() to work. It makes sense in the way you have explained, and not just throwing genes away.

• 0 views • link
written by robjohn7000 robjohn7000

2 answers

You'll need to pay attention to what you are doing. If you are new to R, you will need to do some reading on R data structures, as each behaves differently with regard to indexing. Just guessing, but you probably want:

SigGenes.F[!duplicated(SigGenes.F$genes),]
• 417 views • link
written by Sean Davis Sean Davis

You'r absoultely right. This worked for me as well. Many thanks Sean!

• 0 views • link
written by robjohn7000 robjohn7000

Read ?duplicated:

> x = c(1:10,1:10)
> x
 [1]  1  2  3  4  5  6  7  8  9 10  1  2  3  4  5  6  7  8  9 10
> x[!duplicated(x)]
 [1]  1  2  3  4  5  6  7  8  9 10
>
• 164 views • link
written by Michael Dondrup Michael Dondrup

I used duplicated() this way:

 SigGenes.F[!duplicated(SigGenes.F)]

Got this output:

  Error in `[.data.frame`(SigGenes.F, !duplicated(SigGenes.F)) : 
  undefined columns selected

Then tried:

    SigGenes.F[!duplicated(SigGenes.F[2])]

Output: 

      columns 3:7 have been removed

Thanks

• 0 views • link
written by robjohn7000 robjohn7000

Please consider accepting as an answer and/or upvoting useful answers.

• 0 views • link
written by zx8754 zx8754

Log in to answer this question.

More posts like this