# [R] how can i compute the average of three blocks for each column ?

From: Yen Ngo <yen_h_ngo_at_yahoo.se>
Date: Sun 15 Oct 2006 - 20:22:19 GMT

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)
#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 ###########

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)) }

Regards,

Yen

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