[R] expression set (Bioconductor) problem

[Clayton K Collings]

Hello R people,

>dim(exprs(estrogenrma)

I have an expressionSet with 8 samples and 12695 features (genes)


> estrogenrma$estrogen
  present present absent absent present present absent absent
> estrogenrma$time.h
  10 10 10 10 48 48 48 48

present <- grep("present", as.character(estrogenrma$estrogen))
absent  <- grep("absent", as.character(estrogenrma$estrogen))
ten <- grep("10", as.character(estrogenrma$time.h))
fortyeight  <- grep("48", as.character(estrogenrma$time.h))

present.10 <- estrogenrma[, intersect(present, ten)]
present.48 <- estrogenrma[, intersect(present, fortyeight)]
absent.10 <- estrogenrma[, intersect(absent, ten)]
absent.48 <- estrogenrma[, intersect(absent, fortyeight)]


present.10, present.48, absent.10, and absent.48 are four expression sets
with two samples and 12695 features.

How can I make a new 2 new expressionsets, each have 12695 features and one sample
where 
expressionset1 = (present.10 + present.48) / 2
expressionset2 = (absent.10 + absent.48) / 2
?

Thanks,
Clayton

----- Original Message -----
From: "Tal Galili" <tal.galili at gmail.com>
To: "SML" <parallax at lafn.org>
Cc: r-help at r-project.org
Sent: Thursday, October 6, 2011 4:09:43 AM
Subject: Re: [R] Mean(s) from values in different row?

One way for doing it would be to combine the columns using paste and then
use tapply to get the means.

For example:

set.seed(32341)
a1 = sample(c("a","b"), 100,replace = T)
a2 = sample(c("a","b"), 100,replace = T)
y = rnorm(100)
tapply(y,paste(a1,a2), mean)



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On Thu, Oct 6, 2011 at 8:40 AM, SML <parallax at lafn.org> wrote:

> Hello:
>
> Is there a way to get a mean from values stored in different rows?
>
> The data looks like this:
>  YEAR-1, JAN, FEB, ..., DEC
>  YEAR-2, JAN, FEB, ..., DEC
>  YEAR-3, JAN, FEB, ..., DEC
>
> What I want is the mean(s) for just the consecutive winter months:
>  YEAR-1.DEC, YEAR-2.JAN, YEAR-2.FEB
>  YEAR-2.DEC, YEAR-3.JAN, YEAR-3.FEB
>  etc.
>
> Thanks.
>
> ______________________________________________
> 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.
>

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