load("~/hpc/project/TCGA/pancancer/miRNA/data/TCGA-Pancancer.miRNAseq.RData")
load("~/hpc/methylation/Pancancer/RNA-seq/rnaseqdata.pancancer.RData")

Timeline:

miR23A and TFs: identified and validate TFs binding to miR23A: TransmiR2 + TCGA-co-expression
1470 unique patients with responses to radiation-therapy and 1538 patients with the response to chemotherapy.
When we merge both of them, there are 703 unique patients with clear response to both chemo- and radio-therapy.
2020/01/19: identify all the individual have both chemotherapy and radiotherapy treatment
2020/01/19: immune and targeted therapy response phenotypes were collected with script and saved here
2020/01/17: Dr. Xiong let me check do we have immune and targeted therapy response phenotypes.
2020/01/17: send Dr. Xiong drug responseincluding chemotherapy, radiationtherapy, immune and targeted therapy.
2020/01/14: Updated script, command and code can be found in my Rscript deposition, see and download here
md <- rma(es,slab=source,method = "REML", measure = "SMD",data=output,digits=5,control=list(stepadj=0.5))
2020/01/14: update md/rma command digits and control so that the model fitting can be converged as above

Tcga

Install / Use