How to run the same code for different data?

[kellychan84]

Hello @SteveDenham  your descriptions of my study design are completely correct. I think my experiment design is very simple. Two treatments (1 control and 1 antibiotics), and animals are randomly assigned into two treatments according to RCBD. Now both cecal and fecal samples are collected and are analyzed for microbiota under kingdom, phylum, class, order, family, genus, and species levels. The family, genus, and species levels have so many bacteria that I have to compare them one by one between two treatments. That is the tricky thing.

The percentage data I have converted through excel and can be uploaded to SAS. I here also include my data input code for your reference.

data cecal_family_taxonomy;
  length treatment $20;
  Infile "/home/u39233094/sasuser.v94/Thesis/CSV file/5-family cecal taxonomy for SAS.csv" dlm="," firstobs=5;
  input diet$ treatment$ block pen pig_number Family1 Family1P Family2 Family2P Family3 Family3P Family4 Family4P....Family121P Family122 Family122P TotalR TotalP;     /*species have over 800 bacteria that have to be compared one by one*/                                                                                                                                                                                                                           
run;

[PaigeMiller]

---

@kellychan84 wrote:

My analyses are about gut microbiome. Even though there are large amount of outputs, I have to look through them one by one to see how my positive treatment has an impact on specific bacteria that is under family or species level compared to control group. Even there are over 800 family, I might only find let is say 20 something that have significant differences. Don't know yet. 

---

If you are comparing 800 different families to a control group, you might want to include family in the model itself instead of running 800 separate models, one family at a time.

[kellychan84]

I think GLIMMIX can not include different families in the same one model? Am I wrong?

[SteveDenham]

Yes GLIMMIX can handle multiple levels of family.  There will be missing values, as not every pig will have every taxon group, but that is the sort of thing mixed models are good at handling.  However, your main effect means will not be estimable, so you would look at the simple effect of treatment for each taxon group using the SLICE option of the LSMEANS statement for treatment*family.

SteveDenham

[PaigeMiller]

---

@kellychan84 wrote:

I think GLIMMIX can not include different families in the same one model? Am I wrong?

---

I'm sure you can include a family variable in just about any SAS model.

[MaryA_Marion]

prepare a macro
%macro macroname(parameters)
... your code with parameters referred to as &param_1...&param_2 etc
%mend;