Changes between Version 6 and Version 7 of SOPs/StatisticalSteps

Timestamp:

07/01/20 09:14:03 (5 years ago)

Author:

gbell

Comment:

--

SOPs/StatisticalSteps

@@ -11 +11 @@
 7. Do multiple hypothesis correction (if needed)
 8. Interpret the statistical test
+9. Report the results and the detailed methods
 
 In more detail:
 
 - '''Understand the details of the experiment''' 
-1. What is the big picture; what is begin studied?
+1. What is the big picture? What is begin studied? Why was the experiment performed?
 2. What is the experimental design? Is there biological and/or technical replication?
 3. What measurements were taken?
@@ -28 +29 @@
 1. Are there any obvious problems?
 1. Are there obvious batch effects?
-1. Are there any obvious "outliers" due to some technical reason?
+1. Are there any obvious "outliers" due to some technical (or biological) reason?  Be very careful about removing these (and be prepared to report how/why they were removed).
 1. Could the data need some form of normalization or scaling to make factors more comparable?
 
@@ -43 +44 @@
 
 - '''Organize the data'''
-1. Is the data in a format that can be used by the statistical software?
+1. Is the data in a format that can be used by the statistical software?  R, for example, has a concept of "wide" and "long" data formats.
 1. Does it make sense to scale, normalize, or transform (such as with logs) the data?
 
@@ -52 +53 @@
 
 - ''' Do multiple hypothesis correction'''
-1. If more than one test is performed, you may need multiple hypothesis correction.
+1. If more than one test is performed, you probably need multiple hypothesis correction.
 1. Which is better: Bonferroni, FDR, or another test?
 1. Be prepared to explain why this is necessary.
@@ -61 +62 @@
 1. Does the statistics imply that the result is biologically meaningful (Perhaps the hardest question)?
 
-- ''' Report the statistical test(s)'''
-1. Report in enough detail so that, with the original data, a knowledgeable person could replicate the statistical analysis.
+- ''' Report the results and the detailed methods'''
+1. What figure(s) best displays the data and summarizes the analysis?  Unless there are lots of data points (> 10 or 100, for example), display them all (perhaps along with summary metrics).
+1. Describe and/or show the effect size or another measure of the magnitude of an effect/change (and not just the p-value).
+1. What can be concluded from the analysis?  How generally does this apply?
+1. How many significant figures should be reported?
+1. Report the method with enough detail so that, with the original data, a knowledgeable person could replicate the statistical analysis.
 
 Through all of this, resist any temptation to bias the analysis to produce the result one wants or expects.