Question: Does The Order Of Samples In Cuffdiff Matter?
0
gravatar for skm770
6.6 years ago by
skm770150
skm770150 wrote:

Hi,

We wanted to do fold change using cuffdiff on control_vs_treatment case. What should the order of samples be for input in cuffdiff. Its on the cuffdiff website that :-

FPKMx FPKM of the gene in sample x FPKMy FPKM of the gene in sample y log2(FPKMy/FPKMx) The (base 2) log of the fold change y/x

Currently I am giving cuffdiff with input of control sample and then treatment sample so the genes that are down regulated according to the result are actually upregulated. I just wanted to confirm if reversing the order of sample in cuffdiff would give me different results or not.

thanks

cuffdiff • 2.2k views
ADD COMMENTlink modified 6.6 years ago by Devon Ryan96k • written 6.6 years ago by skm770150
0
gravatar for Devon Ryan
6.6 years ago by
Devon Ryan96k
Freiburg, Germany
Devon Ryan96k wrote:

Yes, reversing the order of the groups will flip the sign of the log2 fold-change.

ADD COMMENTlink written 6.6 years ago by Devon Ryan96k
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