[R] In which order should the p argument within chisq.test() be specified when working in 3 dimensions?

Dear List, I'm in the process of setting up a chi square test with 3 groups (A, B and C). Hence, I have generated an array object like this: my.obj - array(c(overlap_ABC, overlap_AB, overlap_AC, unique_A, overlap_BC, unique_B, unique_C, not_in_any), dim=c(2,2,2)) Now I'm in the process of

Re: [R] heatmap.2 problem

Sorry, I should have added library(gplots) in the beginning of my code On Sun, Jan 13, 2013 at 5:04 PM, Uwe Ligges lig...@statistik.tu-dortmund.de wrote: mycol - colorpanel(n=3,green,grey,red) - - - Peter K Davidsen | MSc, PhD stud. | Centre for Systems Biology | Univ. of Liverpool |

Re: [R] package gplots: (was:) heatmap.2 problem

, tracecol=black, key=FALSE, symm=FALSE, vline=NULL, hline=NULL) Kind regards, Peter On Sun, Jan 13, 2013 at 5:10 PM, Uwe Ligges lig...@statistik.tu-dortmund.de wrote: On 13.01.2013 18:06, Peter Davidsen wrote: Sorry, I should have added library(gplots) in the beginning of my code

[R] heatmap.2 problem

Dear List, I'm trying to generate a simple heatmap that has each row and column separated by a black line. However, for some reason this only happens for the first and last color. The middle color in my colorpanel() command has an addition horizontal and vertical line that I would like to get rid

[R] basic subset question of matrix

Dear list, I would like to subset a large expression matrix based on rownames. That is, I have a list (as a txt-file) with gene names that matches some of the rows in my matrix. I've loaded my matrix as well as gene list using the read.table() command. myMatrix - read.table(name_of_file.txt,

Re: [R] Deleting multiple rows from a data matrix based on exp value

conform to what you mean. HTH, Dennis On Sun, Nov 20, 2011 at 2:45 PM, Peter Davidsen pkdavid...@gmail.com wrote: Dear List, I have a data matrix that consists of ~4500 rows and 25 columns (i.e. an exprSet object that I converted via the 'exprs' function into a data matrix) Now I want

[R] Deleting multiple rows from a data matrix based on exp value

Dear List, I have a data matrix that consists of ~4500 rows and 25 columns (i.e. an exprSet object that I converted via the 'exprs' function into a data matrix) Now I want to remove/delete the rows where all exp. values in that particular row are below or equal to a specific cut-off value (e.g