This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Remove X in row name with only number

Hi Biostars,

I follow this tutorial to perform GSVA: https://alexslemonade.github.io/refinebio-examples/02-microarray/pathway-analysis_microarray_03_gsva.html

They can create a matrix name filtered_mapped_matrix with row names are only number. I convert my column EntrezID to row name and got X before EntrezID, so I would like to remove it. However, this code didn't work.

rownames(your_data) <- gsub("^X", "", rownames(your_data))

Would you please have a suggestion? I can't upload a screenshot here to illustrate as I got this error from Biostar: Exceeded the maximum amount of images you can upload. Thank you so much.

gsva
• 2,666 views • link
updated by Ram Ram • written by Chris • Chris

You don't need to upload the screenshot, you can simply copy-paste the content. Also "code didn't work" is not a sufficient description - was any error message displayed? How did you deduce that the code did not work?

Also, did you check online if rownames can be numeric?

• 0 views • link
written by Ram Ram

There is no error message and nothing changes with the variable your_data. I can't copy and paste a matrix from Rstudio to here that keep the information in the right format. I read that rownames can't start with number but don't know why the tutorial has rownames are only number.

• 0 views • link
written by Chris • Chris

I can't copy and paste a matrix from Rstudio to here that keep the information in the right format.

Yes, you can. Ensure you're only copy-pasting a limited number of rows and columns (10, say):

matrix(round(rnorm(100),2), nrow=10)
       [,1]  [,2]  [,3]  [,4]  [,5]  [,6]  [,7]  [,8]  [,9] [,10]
 [1,]  1.15 -1.47 -1.37 -1.08 -0.19  0.44 -0.16 -1.42  0.39  1.10
 [2,]  1.85 -0.87  0.32  1.78  2.59 -0.75  0.23 -1.36  2.69  0.33
 [3,]  0.79  0.30  1.78 -0.37 -1.38  0.09  0.94 -0.64 -0.57 -1.29
 [4,] -0.53  1.22  2.12 -0.20 -0.66  1.30  0.40  0.52  0.18  0.20
 [5,]  0.11  0.30 -1.52  0.20 -2.80 -0.33  1.14  1.27  1.09  0.20
 [6,] -1.15 -0.63 -0.54 -1.45 -0.52 -0.81  0.32 -0.71  1.55 -0.64
 [7,]  0.35 -0.46  0.28  0.79 -1.05 -0.84 -0.09  0.74  2.86 -1.57
 [8,]  0.06 -0.24  1.24  2.54  0.96  0.64  0.92 -1.40  0.43  0.21
 [9,]  0.29  0.31  1.29 -0.07  0.17  0.69 -0.62  0.69 -0.45  0.85
[10,] -0.29 -1.41  0.31 -0.09 -0.68 -0.13 -0.37  1.14 -2.58 -0.20

don't know why the tutorial has rownames are only number.

Can you point to where this happens in the tutorial, please? Are you speaking about the tibble::column_to_rownames("entrez_id") in section 4.3? If so, they don't seem to care what happens to the Entrez IDs, so why do you care?

• 0 views • link
written by Ram Ram

Yes, section 4.3. Variable: filtered_mapped_matrix. Seem they format Entrez_ID as character with allowing number as rowname. The matrix has thousand of columns so I can't use mouse to select first few rows and columns. It will automatically select all column.

• 0 views • link
written by Chris • Chris

I can't use mouse to select first few rows and columns.

What are you trying to do with the mouse? All you gotta do is run your_data[1:10,1:10] on the Console.

Seem they format Entrez_ID as character with allowing number as rowname.

I don't see them doing that, but you could. Try:

filtered_mapped_matrix <- filtered_mapped_df %>% mutate(entrez_id = as.character(entrez_id)) %>%
  # We need to store our gene identifiers as row names
  tibble::column_to_rownames("entrez_id") %>%
  # Now we can convert our object into a matrix
  as.matrix()
• 0 views • link
written by Ram Ram

Thank you for the suggestion! It turns out that if I use View(your_data), it will show X at the beginning of each rowname but your_data[1:4,1:4] is not. But View(filtered_mapped_matrix), it doesn't show X. Maybe they format Entrez_id as character. Do I need to delete some old images in previous posts to able to upload new images?

       GSM917011  GSM917012  GSM917013  GSM917014
7105   3.861330  3.8247815  5.5487436  3.0800561
64102  0.188879  0.2688151  0.2806487  0.1761636
8813  12.257555 18.8303678 20.3525452 14.8965009
57147  2.074070  3.2011826  3.0844439  2.2441181
• 0 views • link
written by Chris • Chris

Try to get rowname as chracter but still didn't work

rownames(your_data) <- as.character(rownames(your_data))

The rowname in the tutorial is right align, so it is still number. Anyway the row name doesn't have X, it is only how View() work.

       GSM917011  GSM917012  GSM917013  GSM917014
X7105   3.861330  3.8247815  5.5487436  3.0800561
X64102  0.188879  0.2688151  0.2806487  0.1761636
X8813  12.257555 18.8303678 20.3525452 14.8965009
X57147  2.074070  3.2011826  3.0844439  2.2441181
• 0 views • link
written by Chris • Chris 
rownames(your_data) <- as.character(rownames(your_data))

That makes no sense. rownames(your_data) is already a character vector. Are you sure you know what you're doing?

• 0 views • link
written by Ram Ram

Just trying possible solutions. Seem I trying to remove something doesn't exist. But when using View(), it will show in my case but not in the tutorial.

• 0 views • link
written by Chris • Chris

You've isolated the problem to View on Rstudio. Running any R code on the data.frame is not going to help. I ran the following code on Rstudio and it worked without any prefix so you might actually have a different problem:

mat <- matrix(rnorm(100), nrow=10)
rownames(mat) <- 7001:7010
View(mat)

It showed the matrix with no X prefixes. In my experience, the prefixes are added only on import (which can be avoided using check.names=FALSE), so there is some problem at the file or the file-reader level.

• 0 views • link
written by Ram Ram

0 answers

No answers yet.

Log in to answer this question.

More posts like this