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
Thanks for your advice! Since the clinial data varies in cases, I use patients id to represent the difference among patients. As you said, I want to find the difference in TP vs NT while controlling for patient baseline for more exact results, so #2 might be better.