R help - Sep 2009 - How to handle missing values for the GeneMeta package?

Hello all,

It seems that the GeneMeta passage returns NA in the respective row if
any gene in the data sets to be synthesised are missing. Do you know
of a way to overcome this problem?

I tried using the 'impute' package to fill-in the missing values, but
R crashes if 'impute' and 'GeneMeta' packages are used together.
I
have asked a separate question for that.

Thanks
Vassilis

Hi Vassilis --

Vassilis Golfinopoulos wrote:
> Hello all,
> 
> It seems that the GeneMeta passage returns NA in the respective row if
> any gene in the data sets to be synthesised are missing. Do you know
> of a way to overcome this problem?
> 
> I tried using the 'impute' package to fill-in the missing values,
but
> R crashes if 'impute' and 'GeneMeta' packages are used
together. I
> have asked a separate question for that.
Ask questions about Bioconductor packages on the Bioconductor mailing list

  http://bioconductor.org/docs/mailList.html

so you're more likely to get informed answers.

Include a reproducible example to illustrate your problem, so others can
help. For instance
> library(GeneMeta)
> library(impute)
>
No 'crash' so no problem??

Martin
> 
> Thanks
> Vassilis
> 
> ______________________________________________
> 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.

I am not sure if this is the solution you want, but complete.cases  
will remove rows that contain any NA values at all from a matrix.

These lines get rid of NA values in my little function:
	predmat1 <<- as.matrix(predmat[complete.cases(predmat,respmat),])
	respmat1 <<- as.matrix(respmat[complete.cases(predmat,respmat),])

Also, you may want to look into these other options supplied by list  
members:

index <- apply(yourdata, 1, function(x) any( is.na<http://is.na>(x) ) )
yourdata[ !index, ]

or

?na.omit

Sorry if I misunderstood the problem. :)

Payam
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> Hello all,
>
> It seems that the GeneMeta passage returns NA in the respective row if
> any gene in the data sets to be synthesised are missing. Do you know
> of a way to overcome this problem?
>
> I tried using the 'impute' package to fill-in the missing values,
but
> R crashes if 'impute' and 'GeneMeta' packages are used
together. I
> have asked a separate question for that.
>
> Thanks
> Vassilis