Re: [R] spearman correlation and p-value as a matrix

2013-02-14 Thread arun
9010286  NaN  NaN  NaN  NaN  NaN >-0.89010286 >#4  NaN  0.03036290  NaN  NaN  NaN  NaN  NaN  >0.03036290 >#5      NaN  0.08266317  NaN      NaN      NaN      NaN  NaN  >0.08266317 > # Otu00209    Otu00218 >#1  NaN -0.12705

Re: [R] spearman correlation and p-value as a matrix

2013-02-14 Thread Ozgul Inceoglu
317 > # Otu00209    Otu00218 >#1  NaN -0.12705141 >#2      NaN -0.61522514 >#3      NaN -0.89010286 >#4  NaN  0.03036290 >#5  NaN  0.08266317 > >A.K. > > > >- Original Message - >From: Ozgul Inceoglu >To: R help >Cc: >Sent:

Re: [R] spearman correlation and p-value as a matrix

2013-02-14 Thread arun
- Original Message - From: Ozgul Inceoglu To: R help Cc: Sent: Thursday, February 14, 2013 1:10 AM Subject: Re: [R] spearman correlation and p-value as a matrix Thank you all for the answers. I really need to learn a lot. Bu I also discover cor2m(x, y, trim = TRUE, alpha = 0.05) in ecod

Re: [R] spearman correlation and p-value as a matrix

2013-02-14 Thread arun
Dear Ozgul, You could use ?table() or ?count from library(plyr) I assume that you wanted to count only from the first column.  data2<- read.csv("cor3.csv",sep="\t",stringsAsFactors=FALSE)  res1<-as.data.frame(table(data2[,1])) res2<-count(data2[,1]) colnames(res1)<- colnames(res2)  identical(res1,r

Re: [R] spearman correlation and p-value as a matrix

2013-02-13 Thread Ozgul Inceoglu
Thank you all for the answers. I really need to learn a lot. Bu I also discover cor2m(x, y, trim = TRUE, alpha = 0.05) in ecodist package, which gives an output file with significant correlations. Özgül Yj>HI, > >#ag data was created >bg<- as.matrix(read.table(text=" > Otu00022 Otu00029 Otu

Re: [R] spearman correlation and p-value as a matrix

2013-02-13 Thread arun
HI, #ag data was created bg<- as.matrix(read.table(text=" Otu00022 Otu00029 Otu00039 Otu00042 Otu00101 Otu00105 Otu00125 Otu00131 Otu00137 Otu00155 Otu00158 Otu00172 Otu00181 Otu00185 Otu00190 Otu00209 Otu00218 Gi20Jun11  0.001217    0 0.001217    0 0.00    0    0 

Re: [R] spearman correlation and p-value as a matrix

2013-02-13 Thread Jim Lemon
On 02/13/2013 08:48 PM, Ozgul Inceoglu wrote: I have two data matrices that I want to make the correlation between each column from data1 and each column from data 2 and also calculate the p-value Matrices dont have the same size and I tried such a script. bg<- read.table (file.choose(), heade