R help - Feb 2010 - how to do calculations in data matrices?

Please give me just a reference where I can find something useful. 

In summary, I need to :

- find the median of each row of a matrix
- create a new matrix with each value in the first matrix divided by the median
of its row
- if a value "a" in the second matrix is < 1, I need to substitute
it with 1/a

I know that for some of you it must be overeasy, but I swear I googled for two
hours with keywords "operations", "calculations", "data
matrices", "data tables", and "CRAN", and I didn't
find anything useful.

Thank you all


Gabriele Zoppoli, MD
Ph.D. Fellow, Experimental and Clinical Oncology and Hematology, University of
Genova, Genova, Italy
Guest Researcher, LMP, NCI, NIH, Bethesda MD

Work: 301-451-8575
Mobile: 301-204-5642
Email: zoppolig at mail.nih.gov

Some places to start
apply()
sweep()
and any of the good introductory guides to R available online.

For finding R material, it's vastly easier to use the custom search engine
at www.rseek.org than to wander aimlessly around google trying to
find things with "R" in them.

We'd be happy to give more specific answers if you need them,
especially if you do as the posting guide asks and provide
a reproducible example. (Not that you need one for this question,
since you did ask just for references.)

Sarah

On Sat, Feb 13, 2010 at 12:39 PM, Zoppoli, Gabriele (NIH/NCI) [G]
<zoppolig at mail.nih.gov> wrote:
> Please give me just a reference where I can find something useful.
>
> In summary, I need to :
>
> - find the median of each row of a matrix
> - create a new matrix with each value in the first matrix divided by the
median of its row
> - if a value "a" in the second matrix is < 1, I need to
substitute it with 1/a
>
> I know that for some of you it must be overeasy, but I swear I googled for
two hours with keywords "operations", "calculations",
"data matrices", "data tables", and "CRAN", and I
didn't find anything useful.
>
> Thank you all
>
>
> Gabriele Zoppoli, MD
> Ph.D. Fellow, Experimental and Clinical Oncology and Hematology, University
of Genova, Genova, Italy
> Guest Researcher, LMP, NCI, NIH, Bethesda MD
>
> Work: 301-451-8575
> Mobile: 301-204-5642
> Email: zoppolig at mail.nih.gov
> ______________________________________________
> 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.
>


-- 
Sarah Goslee
http://www.stringpage.com
http://www.astronomicum.com
http://www.functionaldiversity.org

On Sat, Feb 13, 2010 at 5:39 PM, Zoppoli, Gabriele (NIH/NCI) [G]
<zoppolig at mail.nih.gov> wrote:
> Please give me just a reference where I can find something useful.
>
To complement Sarah's suggestions, a good place to start is Quick-R [1].
Liviu

[1] http://www.statmethods.net/stats/descriptives.html

Zoppoli, Gabriele (NIH/NCI) [G] <zoppolig <at> mail.nih.gov> writes:
> 
> Please give me just a reference where I can find something useful. 
The others are right that rather than randomly googling, you should bite
the bullet and sit down for a couple of hours with some introductory
material on R (a book, or one of the freely available pdfs). Unless you are
never going to use R again, it will be worth it. But seeing as you asked your
question clearly, here's one
way to do the steps you specify. Hopefully this will help as well.

First, make a matrix to work with:
> mat1 <- matrix(sample(1:10, size=12, replace=TRUE), ncol=4)
> mat1
     [,1] [,2] [,3] [,4]
[1,]    5    7   10    9
[2,]    4   10    8    2
[3,]    8   10    9    5
> 
> 
> In summary, I need to :
> 
> - find the median of each row of a matrix
You can use apply for that:
> row.medians <- apply(mat1, 1, median)
> row.medians
[1] 8.0 6.0 8.5
> - create a new matrix with each value in the first matrix divided by
> the median of its row
That's easy to *do*:
> mat2 <- mat1 / row.medians
> mat2
          [,1]     [,2]     [,3]      [,4]
[1,] 0.6250000 0.875000 1.250000 1.1250000
[2,] 0.6666667 1.666667 1.333333 0.3333333
[3,] 0.9411765 1.176471 1.058824 0.5882353

but it may take more time to understand why that worked. How come it
knew that we wanted to divide each row by the median of the row? (Hint:
understand the "byrow" argument in ?matrix and the mentions of the
word
"recyling" in ?Arithmetic).
> - if a value "a" in the second matrix is < 1, I need to
substitute it
> with 1/a
First make a logical vector which identifies the elements of the matrix
you want to operate on:
> is.small <- mat2 < 1
Then perform the operation on those elements:
> mat2[is.small] <- 1 / mat2[is.small]
> mat2
       [,1]     [,2]     [,3]  [,4]
[1,] 1.6000 1.142857 1.250000 1.125
[2,] 1.5000 1.666667 1.333333 3.000
[3,] 1.0625 1.176471 1.058824 1.700


# you could also use
ifelse(mat2 < 1, 1/mat2, mat2)

dan
> 
> I know that for some of you it must be overeasy, but I swear I googled
> for two hours with keywords "operations",
"calculations", "data
> matrices", "data tables", and "CRAN", and I
didn't find anything
> useful.
> 
> Thank you all
> 
> Gabriele Zoppoli, MD
> Ph.D. Fellow, Experimental and Clinical Oncology and Hematology,
> University of Genova, Genova, Italy
> Guest Researcher, LMP, NCI, NIH, Bethesda MD
> 
> Work: 301-451-8575
> Mobile: 301-204-5642
> Email: zoppolig <at> mail.nih.gov
>