[R] expression set (Bioconductor) problem

[Juliet Hannah]

Note that exprs returns a matrix, so we can manipulate that just as we
would for any other type of matrix. There is also a Bioconductor
mailing list, which may be helpful.

On Thu, Oct 6, 2011 at 4:56 AM, Clayton K Collings <ccolling at purdue.edu> wrote:
> 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)
>
>
>
> ----------------Contact
> Details:-------------------------------------------------------
> Contact me: Tal.Galili at gmail.com |  972-52-7275845
> Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il (Hebrew) |
> www.r-statistics.com (English)
> ----------------------------------------------------------------------------------------------
>
>
>
>
> 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.
>>
>
>        [[alternative HTML version deleted]]
>
> ______________________________________________
> 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.
>
> ______________________________________________
> 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.
>