Changes between Version 13 and Version 14 of FAQ

Timestamp:

05/04/22 09:59:31 (3 years ago)

Author:

gbell

Comment:

--

FAQ

@@ -38 +38 @@
 1. How do I run '''[#tophat_bowtie tophat/bowtie on the LSF with a gzip'd tar (*.tar.gz)]''' file?  [[br]] [[br]]
 1. How can I run '''[#alphafold AlphaFold 2.0]''' here at Whitehead?  [[br]] [[br]]
+1. How can I output '''[#pvalues small p-values]''' from R?  [[br]] [[br]]
 ----
 Answers to Frequently Asked Questions
@@ -222 +223 @@
     * USERNAME     => Username for job submission and email
   * More information, including an explanation of the output files, is here: https://github.com/deepmind/alphafold
+
+1. [=#pvalues How can I output '''small p-values''' from R?]
+  * R often prints small p-values as "p-value < 2.2e-16" whereas the output from the statistical test has actually calculated a much more accurate p-value.
+  * To access the exact p-value, explicitly call the value from the test output.  For example
+{{{
+a = jitter(rep(1, 20))
+b = jitter(rep(3, 20))
+t.test(a,b)  # p-value < 2.2e-16
+t.test(a,b)$p.value  # 9.0e-40 (or another small value, dependent on the output from jitter()
+}}}
+  * Other statistical tests may save the p-value with a different name.  Try names(OBJECT) to see your choices and figure out how to access the exact value.