I have raw read counts of 57 patients ranked with Mandard score as TRG12 and TRG45.
Mandard score : A histological assessment of the response of oesophageal cancers to neoadjuvant treatment (cisplatin chemotherapy and radiotherapy in the original paper). The tumour regression grades were defined as follows: TRG 1 Complete regression - absence of residual cancer and fibrosis extending through the different layers of the oesophageal wall TRG 2 Presence of rare residual cancer TRG 3 An increase in the number of residual cancer cells, but predominantly fibrosis TRG 4 Residual cancer outgrowing fibrosis TRG 5 Absence of regressive changes
Some of these patients have recieved chemotrapy but some of patients recieved chemotrapy + radiotrapy so I considering this as batch but I am not sure if my design is right;
***`My question is: is there any difference TRG12 and TRG45 in terms of gene expression?`*** > head(mycols) condition batch A10 TRG12 A A11 TRG12 B A7 TRG12 A A8 TRG12 A A9 TRG12 B B10 TRG12 B > neu.dds.LRT <- DESeq(dds,betaPrior=FALSE, test="LRT", full=~ batch + condition, reduced=~batch) dpsc.res.LRT <- results(neu.dds.LRT) > resultsNames(dpsc.res.LRT) character(0)
Please correct me if I am wrong
Thanks a lot