R help - Jul 2009 - how to skip a numeric column for averaging other columns?

Data has the first row for variable name and the first column for sample
name. I want to take "Log" for all data, but how to compute without
the
first column for sample name.

That is, 

column 1: sample ID
column 2-10: data

I want to find an average on each column (2-10)
> apply(raw_data,2,mean)
Error in Math.data.frame(list(sample_id = c(1L, 2L, 3L, 4L, 5L, 6L, 7L,  : 
  non-numeric variable in data frame: sample_id

Thank you in advance,

Jin
-- 
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Hi,

On Jul 29, 2009, at 3:02 PM, sandsky wrote:
>
> Data has the first row for variable name and the first column for  
> sample
> name. I want to take "Log" for all data, but how to compute
without
> the
> first column for sample name.
>
> That is,
>
> column 1: sample ID
> column 2-10: data
I think one thing you could/should do in your case is to set your  
rownames to your (I assume) unique sample ID's:

rownames(raw_data) <- raw_data[,1]

Then just nuke that first column:

raw_data <- raw_data[,-1]

But even if you don't do that:
> I want to find an average on each column (2-10)
>
>> apply(raw_data,2,mean)
> Error in Math.data.frame(list(sample_id = c(1L, 2L, 3L, 4L, 5L, 6L,  
> 7L,  :
>  non-numeric variable in data frame: sample_id
You can just run your function over all of the columns *except* the  
first:

apply(raw_data[,-1], 2, mean)

But in this specific case, you can use the specialized colMeans  
function:

colMeans(raw_data[,-1])

-steve

--
Steve Lianoglou
Graduate Student: Computational Systems Biology
   |  Memorial Sloan-Kettering Cancer Center
   |  Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact

log.raw.data <- log(raw.data[,2:10]) I think but I don't understand the  
"Data has the first row for variable name"  comment

--- On Wed, 7/29/09, sandsky <realstone at hotmail.com> wrote:
> From: sandsky <realstone at hotmail.com>
> Subject: [R]  how to skip a numeric column for averaging other columns?
> To: r-help at r-project.org
> Received: Wednesday, July 29, 2009, 3:01 PM
> 
> Data has the first row for variable name and the first
> column for sample
> name. I want to take "Log" for all data, but how to compute
> without the
> first column for sample name.
> 
> That is, 
> 
> column 1: sample ID
> column 2-10: data
> 
> I want to find an average on each column (2-10)
> 
> > log.raw_data=log(raw_data,base=2)
> Error in Math.data.frame(list(sample_id = c(1L, 2L, 3L, 4L,
> 5L, 6L, 7L,? : 
> ? non-numeric variable in data frame: sample_id
> 
> Thank you in advance,
> 
> Jin
> -- 
> View this message in context:
http://www.nabble.com/how-to-skip-a-numeric-column-for-averaging-other-columns--tp24723210p24723210.html
> Sent from the R help mailing list archive at Nabble.com.
> 
> ______________________________________________
> R-help at r-project.org
> mailing list
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> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained,
> reproducible code.
> 

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sandsky ha scritto:
> Data has the first row for variable name and the first column for sample
> name. I want to take "Log" for all data, but how to compute
without the
> first column for sample name.
>
>   
>> log.raw_data=log(raw_data,base=2)
>>     
> Error in Math.data.frame(list(sample_id = c(1L, 2L, 3L, 4L, 5L, 6L, 7L,  : 
>   non-numeric variable in data frame: sample_id
>
> Thank you in advance,
>
> Jin
>   
You are trying to calculate a logarithm for a character variable.
You most probably imported the data with read.table (....header = FALSE).
try

sapply(raw_data, is.numeric)

to see which are the columns that contains "logarithmizable" items

8rino