Chose one condition as control for deltapsi

[Elsa Claude]

Hello,

After reading the doc and doing many tries (and fail) I was wondering if there is a way to force majiq deltapsi to use one specific condition as the control, and the other as a test.

If I'm correct, a negative deltapsi is supposed to show (for exon skipping for example) that the exon is mainly excluded in one condition comparing to the other. My problem is that, I have values that are the opposite of what they are supposed to be : sometimes I have a negative deltapsi, but in bio experiments, it shows that it should be positive.

I have two conditions T5 and unT5. When I do the majiq deltapsi I want the deltapsi to be calculated as unT5 is the control and T5 is the test so the deltapsi should be calculated like : T5 E(PSI) - unT5 E(PSI)

But this is not the case.

I tried to set the test condition as the first group in the majiq delta psi such as (short example) :

majiq deltapsi -grp1 T5_1.majiq T5_2.majiq T5_3.majiq -grp2 unT5_1.majiq unT5_2.majiq unT5_3.majiq -n T5 unT5

I don't understand how am I supposed to do.

Thanks a lot for reading me,

Cheers,

Elsa

[Paul Jewell]

Hello Elsa, 

When I performed a simple test on the workshop data, then I ran the quantifier ($ majiq deptapsi) Changing argument for "-grp1" and "-grp2" around, also flipped the of dpsi. It sounds like this is what you need to do?Can you give an example of the results you are seeing where this swap is not behaving as expected in the output?

Thank you, 

-Paul

[Elsa Claude]

Hi Paul,

Totally ! When I tried, I must have failed something. Not always good to do too much things at the same time I suppose ahah.

Now that I have re-tried with a clear mind, I can see that it is changing, that is true !

Sorry for that !

And thanks again for you help,

Elsa

[Paul Jewell]

Hi Elsa, 

No problem, I'm glad it's resolved. 

Thanks, 

-Paul