R help - Jan 2012 - problem in R

hello sir,
             i m a student of bioinformatics,i hv a problem in R, i want to
do correlation analysis of microarray data,hw can i ignore the "NA"
value
for the calculation or correlation.this is a very large data n many empty
fields they giving me NA values of correlation,wat i do??? please help me.

Regards

MUKUL

	[[alternative HTML version deleted]]

Hi
> 
> hello sir,
>              i m a student of bioinformatics,i hv a problem in R, i want 
to
> do correlation analysis of microarray data,hw can i ignore the
"NA"
value
> for the calculation or correlation.this is a very large data n many 
empty
> fields they giving me NA values of correlation,wat i do??? please help 
me.

What about reading R intro manual which shall be installed in your R/doc 
directory. Or consult help page for the function(s) you want use.

Note especially na.rm or na.action options.

Regards
Petr


> 
> Regards
> 
> MUKUL
> 
>    [[alternative HTML version deleted]]
> 
> ______________________________________________
> 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.

data<-matrix(rnorm(10))
data[c(1,4,6)]<-NA
print(data)
data<-matrix(data[!is.na(data)])
print(data)

-----
----

Isaac
Research Assistant
Quantitative Finance Faculty, UTS
--
View this message in context:
http://r.789695.n4.nabble.com/problem-in-R-tp4260254p4260976.html
Sent from the R help mailing list archive at Nabble.com.

> d <- data.frame(x=c(1,NA,3,4,5), y=c(2,4,6,8,9),
row.names=paste("No.",1:5))
  > predict(lm(y~x, data=d, na.action=na.omit))
  No. 1 No. 3 No. 4 No. 5
    2.2   5.8   7.6   9.4
  > d$y - predict(lm(y~x, data=d, na.action=na.omit))
  [1] -0.2 -1.8 -1.6 -1.4  6.8
  Warning message:
  In d$y - predict(lm(y ~ x, data = d, na.action = na.omit)) :
    longer object length is not a multiple of shorter object length
  > predict(lm(y~x, data=d, na.action=na.exclude))
  No. 1 No. 2 No. 3 No. 4 No. 5
    2.2    NA   5.8   7.6   9.4
  > d$y - predict(lm(y~x, data=d, na.action=na.exclude))
  No. 1 No. 2 No. 3 No. 4 No. 5
   -0.2    NA   0.2   0.4  -0.4

Which do you prefer?

Bill Dunlap
Spotfire, TIBCO Software
wdunlap tibco.com 
> -----Original Message-----
> From: r-help-bounces at r-project.org [mailto:r-help-bounces at
r-project.org] On Behalf Of iliketurtles
> Sent: Wednesday, January 04, 2012 2:15 PM
> To: r-help at r-project.org
> Subject: Re: [R] problem in R
> 
> Michael, thank you for your post, I learned a lot.
> 
> Why is it that people prefer na.exclude to na.omit?
> 
> -----
> ----
> 
> Isaac
> Research Assistant
> Quantitative Finance Faculty, UTS
> --
> View this message in context:
http://r.789695.n4.nabble.com/problem-in-R-tp4260254p4263119.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.