**1.4k**wrote:

I am stuck with a very simple problem. I want to build a Pearson correlation matrix for my microarray dataset. My .cvs file consists of normalized, log-transformed expression values of 18k genes across 36 samples. I want to find the gene-gene Pearson correlation from this matrix using R package. After that, I want to transform the matrix to the form of an edge-list with genes in the first two columns and the value of the correlation in the last column. I was trying out the cor() function in R, but I guess there is some issue with numeric/character values because of which it gives me the error 'x has to be numeric'. Kindly give some suggestions as to what way I can read in the file and transform the matrix.

Thanks

Gene | sample1 | sample2 | sample3 |
---|---|---|---|

A | 10 | 50 | 78 |

B | 50 | 45 | 55 |

C | 70 | 56 | 44 |

**80k**• written 5.2 years ago by pixie@bioinfo •

**1.4k**

I think the cor() function is trying to also use the geneName (column 1) to infer correlations, have you tried

cor(myData[,-1]) to calculate it? Also have a look at the vigniette of the {stats} package!

660Thanks..just a query..as I have to find correlations between A&B..B&C..etc...I read somewhere that R works column wise..so I used cor(t(myData[,-1]))..to transform the matrix...am I doing right ? Another issue is this way I am loosing all the row and column headings ..

1.4kto transpose your data is, in general, just fine. Please have in mind the comment from Istvan Albert.

660