R help - Dec 2010 - Urgent Help with R calculation correlation coefficient

Hi,

I am trying to calculate correlation coefficient for gene expression data.

Tab delimited file looks like this

Id v1   v2    v3
df 56   90    45
gh 87   98    78
ty 89    78    67

I used this code


[code]

gse20437 <-
read.csv("C:/Users//Desktop/data/GSE20437_matrix.txt",header TRUE, sep
= ",", strip.white = TRUE)

gsecor <- cor(gse20437, method ="pearson") or

gsecor <- cor(gse20437)

[/code]

i get error x must be numeric..

can anybody help me.

thanks in advance




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On Mon, Dec 6, 2010 at 11:02 AM, chintan85 <chintanpathak15 at yahoo.com>
wrote:
>
> Hi,
>
> I am trying to calculate correlation coefficient for gene expression data.
>
> Tab delimited file looks like this
>
> Id v1 ? v2 ? ?v3
> df 56 ? 90 ? ?45
> gh 87 ? 98 ? ?78
> ty 89 ? ?78 ? ?67
>
> I used this code
>
>
> [code]
>
> gse20437 <-
read.csv("C:/Users//Desktop/data/GSE20437_matrix.txt",header >
TRUE, sep = ",", strip.white = TRUE)
>
> gsecor <- cor(gse20437, method ="pearson") or
>
> gsecor <- cor(gse20437)
>
> [/code]
>
> i get error x must be numeric..
>
Can you post the following?
str(gse20437)

Liviu
> can anybody help me.
>
> thanks in advance
>
>
>
>
> --
> View this message in context:
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> Sent from the R help mailing list archive at Nabble.com.
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> 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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Hi

r-help-bounces at r-project.org napsal dne 06.12.2010 11:02:03:
> 
> Hi,
> 
> I am trying to calculate correlation coefficient for gene expression 
data.
> 
> Tab delimited file looks like this
> 
> Id v1   v2    v3
> df 56   90    45
> gh 87   98    78
> ty 89    78    67
> 
> I used this code
> 
> 
> [code]
> 
> gse20437 <-
read.csv("C:/Users//Desktop/data/GSE20437_matrix.txt",header
> TRUE, sep = ",", strip.white = TRUE)
> 
> gsecor <- cor(gse20437, method ="pearson") or
> 
> gsecor <- cor(gse20437)
> 
> [/code]
> 
> i get error x must be numeric..
> 
> can anybody help me.
At least your Id column is not numeric. Do not use it for cor.

gsecor <- cor(gse20437[,-1])

Regards
Petr


> 
> thanks in advance
> 
> 
> 
> 
> -- 
> View this message in context: 
http://r.789695.n4.nabble.com/Urgent-Help-with-
> R-calculation-correlation-coefficient-tp3074206p3074206.html
> Sent from the R help mailing list archive at Nabble.com.
> 
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide 
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

On 2010-12-06 02:02, chintan85 wrote:
>
> Hi,
>
> I am trying to calculate correlation coefficient for gene expression data.
>
> Tab delimited file looks like this
>
> Id v1   v2    v3
> df 56   90    45
> gh 87   98    78
> ty 89    78    67
>
> I used this code
>
>
> [code]
>
> gse20437<-
read.csv("C:/Users//Desktop/data/GSE20437_matrix.txt",header >
TRUE, sep = ",", strip.white = TRUE)
>
> gsecor<- cor(gse20437, method ="pearson") or
>
> gsecor<- cor(gse20437)
>
> [/code]
>
> i get error x must be numeric..
If this is so urgent, then wouldn't it seem like a good idea to
actually peruse the help page for read.csv?

If you have a *tab*-delimited file, then why are your using
read.csv??

Try this:
1. read your data with read.table() or read.delim()
2. issue str(gse20437) to see what you've acutally read
3. Note that one of your columns is *not* numeric (as the
    very helpful error message is trying to tell you)

Peter Ehlers
>
> can anybody help me.
>
> thanks in advance
>
>
>
>

Try excluding the first column.

cor(gse20437[, 2:4])


chintan85 wrote:
> 
> 
> Tab delimited file looks like this
> 
> Id v1   v2    v3
> df 56   90    45
> gh 87   98    78
> ty 89    78    67
> 
> I used this code
> 
> 
> [code]
> 
> gse20437 <-
read.csv("C:/Users//Desktop/data/GSE20437_matrix.txt",header >
TRUE, sep = ",", strip.white = TRUE)
> 
> gsecor <- cor(gse20437, method ="pearson") or
> 
> gsecor <- cor(gse20437)
> 
> [/code]
> 
> i get error x must be numeric..
> 
> 
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Sent from the R help mailing list archive at Nabble.com.

On Dec 6, 2010, at 11:28 , Petr PIKAL wrote:
> Hi
> 
> r-help-bounces at r-project.org napsal dne 06.12.2010 11:02:03:
> 
>> 
>> Hi,
>> 
>> I am trying to calculate correlation coefficient for gene expression 
> data.
>> 
>> Tab delimited file looks like this
>> 
>> Id v1   v2    v3
>> df 56   90    45
>> gh 87   98    78
>> ty 89    78    67
>> 
>> I used this code
>> 
>> 
>> [code]
>> 
>> gse20437 <-
read.csv("C:/Users//Desktop/data/GSE20437_matrix.txt",header
> >> TRUE, sep = ",", strip.white = TRUE)
>> 
>> gsecor <- cor(gse20437, method ="pearson") or
>> 
>> gsecor <- cor(gse20437)
>> 
>> [/code]
>> 
>> i get error x must be numeric..
>> 
>> can anybody help me.
> 
> At least your Id column is not numeric. Do not use it for cor.
> 
> gsecor <- cor(gse20437[,-1])
Also, using sep="," for a TAB delimited file is suspect (to say the
least). (Note, by the way read.delim())


-- 
Peter Dalgaard
Center for Statistics, Copenhagen Business School
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Phone: (+45)38153501
Email: pd.mes at cbs.dk  Priv: PDalgd at gmail.com