And was it it?
Rui Barradas
Em 05-10-2012 21:44, genome1976 escreveu:
Thanks Rui.I actually exactly did that.
Date: Fri, 5 Oct 2012 05:49:20 -0700
From: ml-node+s789695n4645154...@n4.nabble.com
To: genome1...@hotmail.com
Subject: Re: Calculating all possible ratios
Hello,
Comment
Thanks Rui.I actually exactly did that.
Date: Fri, 5 Oct 2012 05:49:20 -0700
From: ml-node+s789695n4645154...@n4.nabble.com
To: genome1...@hotmail.com
Subject: Re: Calculating all possible ratios
Hello,
Comment out the second apply and all following instructions using 'r2'.
In the
Hello,
Comment out the second apply and all following instructions using 'r2'.
In the end return 'r1', not cbind.
Hope this helps,
Rui Barradas
Em 04-10-2012 23:38, genome1976 escreveu:
Hi Rui,
A while ago you helped me with calculaing all possible ratios from a dataset.
This is the co
Hi Rui,
A while ago you helped me with calculaing all possible ratios from a dataset.
This is the code I am using as suggested by you.
data <- read.table("new_data.txt", header=T, row.names=1, sep="\t")
pairwise.ratios <- function(x, prefix="probeset", char=":"){
n <- ncol(x)
ces of the same dimensions.
Hope this helps,
Rui Barradas
Em 15-05-2012 11:00, r-help-requ...@r-project.org escreveu:
Date: Mon, 14 May 2012 05:49:33 -0700 (PDT)
From: genome1976
To:r-help@r-project.org
Subject: Re: [R] Calculating all possible ratios
Message-ID:
Content-Type: text/plain
Hi Ru
Hi Rui,
Thanks once again for all the help. I need to ask for one more help from you. I
have two matrices, with probesets as rows and samples as columns.
The samples in the two matrices are matched (from the same animal but two
different tissues). I want to create a correlation matrix of sample
I apologize. You were right.
You are a genius!
Thanks so much!
Best Regards,
Som.
Date: Sat, 12 May 2012 15:20:52 -0700
From: ml-node+s789695n4629656...@n4.nabble.com
To: genome1...@hotmail.com
Subject: RE: Calculating all possible ratios
Hello,
Nothing wrong with me, maybe your R
Hi Rui,
Thanks once again. I really appreciate it.
I tried using the code with the following dataset:
Sample
P1
P2
P3
P4
P5
P6
P7
P8
P9
P10
S1
5292.9
605.1
5213.9
1710.6
1407.8
1079.4
1379.6
9321.4
6951
1205.8
S2
104.6
57.129
625.
Hello,
Nothing wrong with me, maybe your R session has some conflicting objects.
Running the function in the previous post on the first 4 rows and first 6
columns of your dataset the result was (copy&paste to your session)
result <- structure(c(8.74714923153198, 1.83094400392095, 9.92065138471113
Hello,
I'm glad it helped. Now to make the result readable. (I had thought of it.)
pairwise.ratios <- function(x, prefix="probeset", char=":"){
n <- ncol(x)
cn <- colnames(x)
if(length(cn) == 0){
cn <- gsub(" ", "0", formatC(seq.int(n), width=nchar(n)))
Thanks so much Rui. I really appreciate all the help.
I implemented the code and it ran fine. I was wondering how I could include the
probeset ids as probeset1:probeset2 in the final output so that I know which
ratios are for which probeset pairs.
Thanks so much.
Som.
Date: Sat, 12 May 2012 0
Hello,
If by all possible gene ratios you mean all pairwise column ratios, try
the following.
# Make up some data
x <- matrix(1:24, ncol=6)
cmb <- combn(ncol(x), 2)
r1 <- apply(cmb, 2, function(j) x[, j[1]]/x[, j[2]])
r2 <- apply(cmb, 2, function(j) x[, j[2]]/x[, j[1]])
cbind(r1, r2)
Note th
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