cwyoo wrote:Using this master file, we perform various case control analyses, such as:
1. Normal-8 samples to basal-71 samples
2. 8 normal to 53 her2 rich
3. 8 normal to 217 luminal A
4. 8 normal to 111 luminal B
5. 71 basal to 217 luminal A
6. 71 basal to 111 luminal B
7. 71 basal to 53 HER-enriched
8. 463 cases (samples) where we combine all subtypes into a variable called PAM50_Subtype
This is a dataset that was created by identifying 933 genes that are significantly correlated with NRF1 (r > 0.09191, p < 0.05, see my posting under: Board index ‹ Analyses & Results ‹ Others ‹ Breast Cancer ‹ Datasets, posted on Tue Mar 03, 2015 8:14 pm (
http://131.94.9.17/phpbb/viewtopic.php?f=49&t=50&start=40#p359) how we calculated the p value.
Also this dataset introduces PAM50_Subtype which codes the following number of subtypes: 8 Normal-like (coded as 0), 81 Basal-like (coded as 1), 209 Luminal A (coded as 2), 112 Luminal B (coded as 3), and 53 HER2-enriched (coded as 4)