Entering edit mode
4.3 years ago
jeannine.diesch
▴
10
Hi,
I want to use expression datasets from TGCA to determine if there is a correlation between my gene of interest and a specific gene list (containing 40-50 different genes). Here's an example of such a expression dataset (although in reality with many more columns and rows)
Gene Sample1 Sample2 Sample3 Sample4
1 A 22.1470 171.2680 20.9980 6.4587
2 B 220.9870 100.6290 174.0080 151.4630
3 C 2.4178 10.1597 0.7311 1.7212
4 D 177.4080 371.3640 295.6750 127.4830
5 E 15911.5000 1494.3300 1333.5700 2424.2600
6 F 0.4836 0.4838 36.5564 6.8847
7 G 118.9560 22.2545 16.0848 75.7315
8 H 0.0000 0.4838 0.0000 0.4303
So for example I want to calculate the correlation of gene A with module1 containing genes D, E, F, H. How would I do this, for example in R?
Any help would be highly appreciated!
Subset the TCGA expression for your gene of interest and then find out the correlation.