log2() and -min() very quick question
The second line is just scaling the data based on log2. It is subtracting the minimun of the entire matrix (not just each row) and adding 1 to make sure there is not a value of zero since log2(0) is not valid. Here is an example of sample data:
x <- matrix(runif(25, -50, 50), 5) x
[,1] [,2] [,3] [,4] [,5] [1,] 29.730883 15.47239 -28.679186 47.617069 -48.692242 [2,] -4.472555 -14.68027 -37.062765 23.179251 21.556607 [3,] -8.991592 -22.97399 -2.188197 -14.327309 -39.681576 [4,] 31.087024 49.26841 42.407447 -6.852631 -5.371565 [5,] 10.493329 13.34933 9.876097 -35.178844 14.010105
# scale to log2 x <- log2(x - min(x) + 1) x
[,1] [,2] [,3] [,4] [,5] [1,] 6.311487 6.026017 4.393214 6.604506 0.000000 [2,] 5.498879 5.129776 3.658723 6.187283 6.154795 [3,] 5.346980 4.739754 5.569978 5.144248 3.323466 [4,] 6.335913 6.628783 6.525124 5.420873 5.469908 [5,] 5.911346 5.978232 5.896474 3.859313 5.993275 You should see a noticable change between the data read in and the result of the second statement.
On Mon, Jun 13, 2011 at 11:59 AM, Ben Ganzfried <ben.ganzfried at gmail.com> wrote:
I'm looking over good-code a post-doc in my lab wrote and trying to learn
how it works. ?I came across the following:
rel.abundance <- as.matrix(read.delim("rel.abundance.csv",row.names=1,as.is
=TRUE))
rel.abundance <- log2(rel.abundance-min(rel.abundance)+1)
I'm not sure what the second line is doing. ?I ran each line in R and
couldn't see a noticeable difference in the output. ?I assume log2() takes
the log base 2 of the values? ?I'm not clear what -min(rel.abundance) is
doing either...my hunch would be that it would take the smallest value in
each row?
I'd really like to figure out:
1) What's actually going on?
2) Is there a good way to run a command over a large dataset in R and better
be able to tell what is going on? ?More specifically, when I run each line
in R it looks something like this (w/ dif. values per row):
Archaea|Euryarchaeota|Methanobacteria|Methanobacteriales|Methanobacteriaceae|Methanobrevibacter,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,3,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,3,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,23,0,3,0,0,0
There are a lot of cells w/ values per row, which is one reason why I think
it is difficult to detect a pattern....
Thanks in advance!
Ben
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