MOCCASIN model matrix doubts - particular case

[Miriam Martínez]

Hi biociphers team!

Right now I'm in the middle of analyzing my data, but I have some particular doubts regarding moccasin model matrix and command and I was wondering if you could help me a bit.

To have some context: I am preparing a model matrix with an intercept for the following confounders (gender, male 1 female 0; batches (6 batches but leaving one out on the matrix, so 5 columns of batches); RIN and age (three  groups, and also leaving one out, so 2 columns). In an older post Barry gave me some more detailed insights on how moccasin worked, but when having to set the command, I'm getting confused. My main objective is to remove the confounding effects of these variables from my analysis, but I'm not sure if for doing that I need to remove all the effects in the adjustment and not enforcing any of the factors (mainly with gender, the different batches and age). 

Regarding RIN, in the old post I commented, I read this phrase: "In fact, as of now, the coming major update to MAJIQ (MAJIQ V3) does not include the option to set adjusted values for confounders, which makes including the intercept effectively required to get meaningful results for most use-cases. It also adds to the need for users to consider transforming confounding factors before executing Moccasin so that the adjusted value of 0 is desirable (e.g. 10 - RIN rather than RIN)." Therefore I was wondering how should I add my RIN data to the model matrix now and how should I set up the command to model my data to high quality RINs (10). 

I hope that everything is clear and if you need me to clarify something, please let me know. Thank you very much in advance for your help as always.

Best,

Miriam

[bsl...@seas.upenn.edu]

I have been in direct discussions with Miriam, and this has led me to update the MOCCASIN documentation with advice that relates to her questions and can help MOCCASIN users more generally: please see https://biociphers.bitbucket.io/majiq-docs/getting-started-guide/moccasin.html#tips-for-setting-up-your-model-matrix

Best Regards,

Barry