Hi!

I've downloaded HTSeq-Counts of 48 patients from TCGA, all of the patients have a NT aliquot and a TP aliquot，I want to find the DEGs of two conditions using DESeq2,

myfactor is:

> head(myfactor)
  patient tissue
1       1     NT
2       2     NT
3       3     NT
4       4     NT
5       5     NT
6       6     NT
> tail(myfactor)
   patient tissue
91      43     TP
92      44     TP
93      45     TP
94      46     TP
95      47     TP
96      48     TP

now I have alternative in design of DESeqDataSetFromMatrix().

DEA_DESeq<-DESeqDataSetFromMatrix(countData = count, colData = myfactor,design=~tissue)  #1
DEA_DESeq<-DESeqDataSetFromMatrix(countData = count, colData = myfactor,design=~patients+tissue)   #2

So which design is better?

I appreciate your help，

Yang

If you want to find the difference in TP vs NT while controlling for patient baseline, you would provide the patient variable in the design (e.g. #2 above).

The question of what design is more about your goals in the analysis. I'm just guessing based on your mentioning the patient ID that you likely want to control for patient baseline, but these choices are up to you as the analyst. The support site is more for questions about the software and how to use it, and not intended for statistical consultation about what is the appropriate design for a given dataset.