[R] Odp: Urgent Help with R calculation correlation coefficient

[peter dalgaard]

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
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Email: pd.mes at cbs.dk  Priv: PDalgd at gmail.com