JMP Genomics ANOVA and One-way ANOVAHi, I am using ANOVA and One-way ANOVA in JMP Genomics for simple RNAseq analysis where we compare two groups. The p-values are quite different from each other in both analyses, and also we have not been able to replicate them in R packages. It would greatly help to know e.g. which ANOVA or One-way ANOVA approach is used (e.g. Wilcoxon).
1) Why would the results differ for the ANOVA and One-way ANOVA?
2) Where can I find more information on exactly which ANOVA method is used?
Thank you so much for your consideration. I hope my question makes sense.
AnalyticsRe: JMP Genomics ANOVA and One-way ANOVAHi @AS ,
Which version of JMP Genomics are you using by the way?
JMP Genomics user guide might assistance in answering these questions. Take a look here. It is a description of One-way ANOVA and how it compares to ANOVA. It includes which SAS PROCs are used.
The p-values will differ from the many packages in R which implement one-way ANOVA and ANOVA in different ways. Take DESeq2 for example. To get a similar result to DESeq2, make sure that the option Shrink variances using Empirical Bayes it turned on within the Options tab of the One-way ANOVA dialog box. This will be the main difference between different R packages and JMP Genomics. There will also be differences in application of Multiple Test Correction methods as well.
I hope that helps.
Re: JMP Genomics ANOVA and One-way ANOVAHi Chris, thanks for your fast feedback and consideration. I am using JMPGenomics 9, with JMP13.2.1.
A colleague of mine just used R base function aov to try to replicate the one-way anova results with the same expression values I had used and was not able to replicate them, but taking it from your advice I think there some settings which are different. I ran ANOVA (with diagnosis as fixed effect) and One-way ANOVA from within JMPGenomics and get different results for the p-values. Not sure what to use. Would you have advice how to chose the most suitable method? This might be hard to tell, without knowledge of all the settings.
