Re: [R] mplot :how to deal with missing data

From: Jim Lemon <bitwrit_at_ozemail.com.au>
Date: Fri 03 Jun 2005 - 08:42:11 EST

NATALIA F TCHETCHERINA wrote:
> Hello all,
> I have data:
>
> Genes time rep vart dye y trt
> 130911 sa1-d07 030min 1 col g 9.636244 o
> 145771 sa1-d07 030min 1 col r 8.107577 c
> 93335 sa1-d07 030min 1 ler g 7.409566 o
> 94821 sa1-d07 030min 1 ler r 5.107160 c
> 10119101 sa1-d07 030min 2 col g 8.336862 o
> 11605101 sa1-d07 030min 2 col r 7.824530 c
> 725313 sa1-d07 030min 2 ler g 8.249347 o
> 740171 sa1-d07 030min 2 ler r 7.565084 c
> 1160522 sa1-d07 030min 3 col g NA c
> 1011922 sa1-d07 030min 3 col r NA o
> 562232 sa1-d07 030min 3 ler g 9.974227 c
> 547362 sa1-d07 030min 3 ler r 10.341149 o
> ..................................................
> ..................................................
> ..................................................
>
> I would like to get graphs means for two-way factor combinations
> I used Rlab package:
>
>>mplot(data$y[which(data$Genes==sa1-d07)],
>
> data$time[which(data$Genes==sa1-d07)], data$trt[which(data$Genes==sa1-d07)])
>
> However, I have the following error message:
>
> plot window will lay out plots in a 3 by 1 matrix
> Error in plot.window(xlim, ylim, log, asp, ...) :
> need finite 'ylim' values
> In addition: Warning messages:
> 1: no finite arguments to min; returning Inf
> 2: no finite arguments to max; returning -Inf
>
> I think this is because of some y='NA'.
> My question is: how I can deal with this problem?

Hi Natalia,

Your problem is that the character variable "genes" should be enclosed in quotes:

mplot(data$y[which(data$Genes=="sa1-d07")],
   data$time[which(data$Genes=="sa1-d07")],
   data$trt[which(data$Genes=="sa1-d07")])

or a bit more neatly:

which.genes<-data$Genes=="sa1-d07"
mplot(data$y[which.genes],data$time[which.genes],data$trt[which.genes])

Without the quotes, the interpreter reads the value as sa1 - d07, and since it cannot find an object named sa1, returns no values. Also, "data" is not an ideal name for your data frame.

Jim



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