R help - Oct 2006 - how can i compute the average of three blocks for each column ?

Dear all, 
   
   
  I want to compute the average of the three blocks for each x-variable which is
equal slide in the code below. How can I do that ?
   
   
  block  x1    x2    x3    x4    x5
  1        23    22   23    24    23
  1        21    25   26    21    39
  1        23    24    22    23   23
  2        20     21   23    24    28
  2       32     23    34     24   26
  2       19     34    34    13    34
  3       12     32  ´ 23    34    19
  3       23      24   25    26    27
  3       12     78   23    24    24
   
   
  # read table of data for this slide=(x1)
  a<-read.table(file =
slide[i],header=T,sep='\t',na.strings="NA")
  #length(a$ID)
  #Eleminate Neg. and Pos. controls from the dataset. The logical negation of
the "%in%" function,
  #tells subset to only select those row where the "ID" column does
not contain either "empty" or "none"
  new <- subset(a,!ID %in% c("empty","none","
"))
  #length(new$ID)
  #new[1:20,c(1,4,5,9)]
   
   
  #five first columns give position identifiers, include a column with block
  layout=new[,1:5]
  layout[1:30,]
   
  #9th columns which give the median foreground =values of x-variables
  fg1=as.matrix(new[,9])
  length(fg1)
  mean(fg1)  # calculate the mean of x1
   
   
   
  #### I try to do something like :##########
   
  block1=fg1[layout$Block==1,]
  block2=fg1[layout$Block==1,]
  block2=fg1[layout$Block==1,]
  average=(block1+block2+block3)/3
   
  but it did not work.
   
  ################## How can i calculate the means of remaining x_variables?
  #########   Read data for the remaining slides =x2,x3,x4,x5  ###########
   
  for (i in 2:num.slides){
  na1 <- strsplit(na[[i]][k],".txt")
  na2 <- strsplit(na1[[1]][1],"-")
  bat=na2[[1]][1]
  sli=na2[[1]][2]
  nslide <- cbind(nslide,as.numeric(sli))
  # nslide is a vector giving the number of the slide in the batch
  # read table of data for this slide
 
a<-read.table(file=slide[i],header=T,sep='\t',na.strings="NA")
  new<- subset(a,!ID %in% c("empty","none","
"))
  # append FG data to the matrices containing the slides already read
  fg1=cbind(fg1,as.matrix(new[,9]))
  }
   
  colnames(fg1)=nslide
  fg<-data.frame(peptide=c(new$Name),fg1)
  fg <- edit(fg)
   
   
   
  ##### Another question : I have three graphs which are displayed one after one
with a large space between them. Can I move these graph closer each other by
making them bigger and how ? Below is the code that i have written for plotting
the graphs.
   
  par(mfrow=c(3,1))
for (j in 1:3)
{
boxplot(split(pos$y[pos$Block==j],pos$Slide[pos$Block==j]),
col="lightgray", cex=.65, outline=TRUE, main=paste("Positive
Controls Block",j))
}

   
  Thank you for your help,
  Regards,
   
  Yen

	[[alternative HTML version deleted]]

Hi

I haven't seen any answer yet so I try
>From your not very clear explanation I suspect you want to do some 
block aggregation
> test
  block x1 x2 x3 x4 x5
1     1 23 22 23 24 23
2     1 21 25 26 21 39
3     1 23 24 22 23 23
4     2 20 21 23 24 28
5     2 32 23 34 24 26
6     2 19 34 34 13 34
7     3 12 32 23 34 19
8     3 23 24 25 26 27
9     3 12 78 23 24 24
> by(test[,-1], test$block, mean)
test$block: 1
      x1       x2       x3       x4       x5 
22.33333 23.66667 23.66667 22.66667 28.33333 
-----------------------------------------------------------------------------------------------------
test$block: 2
      x1       x2       x3       x4       x5 
23.66667 26.00000 30.33333 20.33333 29.33333 
-----------------------------------------------------------------------------------------------------
test$block: 3
      x1       x2       x3       x4       x5 
15.66667 44.66667 23.66667 28.00000 23.33333 
> aggregate(test[,-1], list(test$block), mean)
  Group.1       x1       x2       x3       x4       x5
1       1 22.33333 23.66667 23.66667 22.66667 28.33333
2       2 23.66667 26.00000 30.33333 20.33333 29.33333
3       3 15.66667 44.66667 23.66667 28.00000 23.33333
>
Regarding your second question with plotting see arguments in par, 
especially mar or mai.

HTH
Petr

On 15 Oct 2006 at 22:22, Yen Ngo wrote:

Date sent:      	Sun, 15 Oct 2006 22:22:19 +0200 (CEST)
From:           	Yen Ngo <yen_h_ngo at yahoo.se>
To:             	r-help at stat.math.ethz.ch
Subject:        	[R] how can i compute the average of three blocks for each
column ?
> Dear all, 
> 
> 
>   I want to compute the average of the three blocks for each
>   x-variable which is equal slide in the code below. How can I do that
>   ?
> 
> 
>   block  x1    x2    x3    x4    x5
>   1        23    22   23    24    23
>   1        21    25   26    21    39
>   1        23    24    22    23   23
>   2        20     21   23    24    28
>   2       32     23    34     24   26
>   2       19     34    34    13    34
>   3       12     32  ? 23    34    19
>   3       23      24   25    26    27
>   3       12     78   23    24    24
> 
> 
>   # read table of data for this slide=(x1)
>   a<-read.table(file =
slide[i],header=T,sep='\t',na.strings="NA")
>   #length(a$ID) #Eleminate Neg. and Pos. controls from the dataset.
>   The logical negation of the "%in%" function, #tells subset to
only
>   select those row where the "ID" column does not contain either
>   "empty" or "none" new <- subset(a,!ID %in%
c("empty","none"," "))
>   #length(new$ID) #new[1:20,c(1,4,5,9)]
> 
> 
>   #five first columns give position identifiers, include a column with
>   block layout=new[,1:5] layout[1:30,]
> 
>   #9th columns which give the median foreground =values of x-variables
>   fg1=as.matrix(new[,9]) length(fg1) mean(fg1)  # calculate the mean
>   of x1
> 
> 
> 
>   #### I try to do something like :##########
> 
>   block1=fg1[layout$Block==1,]
>   block2=fg1[layout$Block==1,]
>   block2=fg1[layout$Block==1,]
>   average=(block1+block2+block3)/3
> 
>   but it did not work.
> 
>   ################## How can i calculate the means of remaining
>   x_variables? #########   Read data for the remaining slides
>   =x2,x3,x4,x5  ###########
> 
>   for (i in 2:num.slides){
>   na1 <- strsplit(na[[i]][k],".txt")
>   na2 <- strsplit(na1[[1]][1],"-")
>   bat=na2[[1]][1]
>   sli=na2[[1]][2]
>   nslide <- cbind(nslide,as.numeric(sli))
>   # nslide is a vector giving the number of the slide in the batch #
>   read table of data for this slide
>  
a<-read.table(file=slide[i],header=T,sep='\t',na.strings="NA")
new<-
>   subset(a,!ID %in% c("empty","none"," ")) #
append FG data to the
>   matrices containing the slides already read
>   fg1=cbind(fg1,as.matrix(new[,9])) }
> 
>   colnames(fg1)=nslide
>   fg<-data.frame(peptide=c(new$Name),fg1)
>   fg <- edit(fg)
> 
> 
> 
>   ##### Another question : I have three graphs which are displayed one
>   after one with a large space between them. Can I move these graph
>   closer each other by making them bigger and how ? Below is the code
>   that i have written for plotting the graphs.
> 
>   par(mfrow=c(3,1))
> for (j in 1:3)
> {
> boxplot(split(pos$y[pos$Block==j],pos$Slide[pos$Block==j]),
> col="lightgray", cex=.65, outline=TRUE, main=paste("Positive
Controls
> Block",j)) }
> 
> 
>   Thank you for your help,
>   Regards,
> 
>   Yen
> 
>  [[alternative HTML version deleted]]
> 
> 
Petr Pikal
petr.pikal at precheza.cz