Re: New submission from zkamvar.netlify.app/

[Vanina Castroagudin]

Dear Zhian,

I am very sorry to bother you again with a question about Popp-R. But I wasn't find anything in the manuals od vignettes that would help me. 

I made and IA calculation and obtained the results in the figure attached. The p-value obtained is p= 0.892, but as you can see in the histogram it is in the LEFT tail of the distribution (negatives values) so.. DO I HAVE TO REPORT THIS P VALUES AS 1-PVALUE OBTAINED? I mean, the correct value to report would be p= 1- 0.892 = 0.108.

All your examples have the p-value on the right tail, I don't know I am getting it in the left tail.

Thanks in advance,

Vanina

On Fri, Jul 16, 2021 at 3:52 PM Zhian Kamvar <zka...@gmail.com> wrote:

Hi Vanina,

I've sent a response to the forum. I apologize for the delay. My internet was out when you sent it and I only recently regained my connection, so I've fallen behind on my volunteer projects.

Best,

Zhian

On Jul 15, 2021, at 16:04 , Formspree <nor...@formspree.io> wrote:

New form submission Someone just submitted a form using formspree.io. Woo! name Vanina Castroagudin email v.castr...@gmail.com message Hello Dr Kamvar,  I have two questions about Poppr and data management, and I was wondering if you can help me with them. I read the package manual and literature but I was not able to find the answers.  1- Is it the same to enter the data for pop analysis with SSR as fragment size or the number of repeats? Are the analyses going to give me the same answers?  2- How can I distinguish a null allele ( no repeats) for the missing data (usually represented with a zero) ?  Thanks in advance.  Vanina  Submitted 11:04 PM - 15 July 2021 Mark as spam     You are receiving this because you confirmed this email address on Formspree. Don't want these emails anymore? No problem! Simply remove the form on formspree.io or unsubscribe from this form's notifications.

--

Vanina L. Castroagudín, PhD

Visiting Research Scientist

Mycology & Nematology Genetic Diversity & Biology Laboratory

USDA - ARS

10300 Baltimore Avenue, Bldg 10A, Room 227

Beltsville, MD 20705

Cell: (479) 313-3780

Vanina.Ca...@usda.gov

v.castr...@gmail.com 

[Zhian N. Kamvar]

Hi Vanina,

Negative values of this index are not uncommon. You should report the p-value as-is since this is a one-sided test.

One factor that should be considered is that you have 5 samples in this result, which limits your ability to detect linkage. For more information on that, the last (unpublished) chapter of my dissertation looked at what factors influence negative values of the index of association: https://raw.githubusercontent.com/zkamvar/clonal-inference-simulations/master/manuscript/clonal-inference.pdf

All the best,
Zhian