I can’t reproduce these p-values from a PloS Medicine article (Am I missing something obvious?)

So I was trying to find an article with statistics in it that I could have my intro stats students reproduce as an assignment.  So I went to PloS Medicine and randomly chose a recent paper.  I can across this one: http://journals.plos.org/plosmedicine/article?id=10.1371/journal.pmed.1001807#pmed-1001807-t001

I was going to have my student reproduce the numbers in this paragraph in the results section:

As described above, GII VLPs were distinct from the GI VLPs at 7 d post-vaccination. Interestingly, the GII.4C VLP (representing the vaccine component) associated much more closely with the early GII.4 VLPs than with either the late GII.4 VLPs or the GII VLPs from other genotypes (ANOVA: F2,4 = 14.74, p = 0.0143), showing that the IgG response to GII.4C vaccination is highly cross-reactive with the early GII.4 VLPs but not the antigenically distinct contemporary GII.4 VLPs or other GII VLPs. Even as late as 180 d post-vaccination (Fig. 9G–I), clustering by genogroup (or by subclades within genogroups) remained (t-test: t53 = 23.96, p < 0.001), although overall distances (dissimilarities) in IgG responses differentiating between VLPs had decreased compared to day 7. Specifically, the GI viruses clustered relative to the other virus strains (t25 = 11.32, p = 0.0024), GII.4C continued to cluster with GII.4.1997 and GII.4.2002 (t25 = 8.973, p = 0.0061), and the contemporary GII.4 VLPs remained tightly clustered with the other GII genotypes (t38 = 19.24, p < 0.001). Interestingly, and echoing our findings above, GII.4.1997 remained somewhat distinct from GII.4C and GII.4.2002 (Fig. 9G–I) because of the elevated levels of IgG against GII.4.1997 VLP still found in several of the vaccine recipients 6 mo post-vaccination.

…but I can’t reproduce the numbers myself.  I can reproduce the p-value for the ANOVA (0.0143), but I can’t reproduce any of the p-values for the t-tests.  For instance, with a t-test statistic of 8.973 with 25 degrees of freedom, I get a two-sided p-value of 0.00000000272 as opposed to the stated p-value of 0.0061.  Am I missing something obvious?  Or are these p-values all wrong?

Follow-up question: If (IF!) the p-values are all wrong, as I suspect, should I still assign it to my students and ask them to reproduce the numbers as a lesson that they shouldn’t trust every statistics they see?

Cheers!

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NY Teachers’ Unions Urge Parents To Opt Children Out Of Common Core Tests

Originally posted on CBS New York:

NEW YORK (CBSNewYork) — Teachers’ unions are encouraging parents to opt out of taking the Common Core standardized tests that begin on this week.

As WCBS 880’s Sophia Hall reported, starting on Tuesday students across New York in grades three through eight are set to start taking the controversial Common Core tests.

Using robo-calls, the United Teachers Union has called on parents to opt their kids out of the tests.

[cbs-audio-player title=”NY Teachers’ Unions Urge Parents To Opt Children Out Of Common Core Tests” artist=”WCBS” download=”false” image=”https://cbsnewyork.files.wordpress.com/2014/08/classroom_common_core.jpg” url=”https://cbsnewyork.files.wordpress.com/2015/04/ny-skl-tests-hall.mp3″ station_name=”Sophia Hall reports” station_logo=”https://cbsnewyork.files.wordpress.com/2014/12/880-audiographic.jpg”]

Meanwhile, some superintendents have warned that if too many students opt out, districts will lose state funding.

Teachers have said they should not be evaluated on the scores because they are unreliable and do not account for many factors, including poverty. And many parents believe the tests are too stressful for children.

Supporters, however, believe it provides useful information of the…

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8 remaining NCAA kaggle scenarios

Final Four: Kentucky, Wisconsin, Duke, Michigan State

Kentucky beats Duke: Yosarian, ZachB, 7

Duke beats Kentucky: Pookie, Juho, 4

Kentucky beats Michigan St: Yosarian, ZachB, 13

Michigan State beats Kentucky: Juho, One Shining MGF, 2

Wisconsin beats Duke: Monte, ZachB, 6

Duke beats Wisconsin: ZachB, Monte, 4

Wisconsin beats Michigan State: ZachB, Wally, 15

Michigan State beats Wisconsin: Wally, ZachB, 3

Kaggle March Madnes Machine Learning Scenarios with 6 games remaining

We. Are. Still. Alive.

Disclaimer: I’m not guaranteeing that everything here is correct.  Please verify everything for yourself if you plan on using this information to hedge.

Scenarios where we finish first

There are only 32 possible scenarios left for the rest of the NCAA tournament.  There are two scenarios that would make us repeat champions.

1.) Final Four of Kentucky, Wisconsin, Gonzaga, and Michigan State with Gonzaga beating Kentucky in the finals.

2.) Final Four of Kentucky, Wisconsin, Gonzaga, and Louisville with Gonzaga beating Kentucky in the finals.

Scenarios where we finish second

There are three scenarios that we finish second in:

1.) Final Four of Kentucky, Wisconsin, Gonzaga, and Louisville with Gonzaga beating Wisconsin in the finals.

2.) Final Four of Kentucky,Wisconsin, Duke, and Louisville with Louisville beating Kentucky in the finals.

3.) Final Four of Kentucky,Wisconsin, Duke, and Michigan State with Michigan State beating Kentucky in the finals.

Some notes

  • If Duke wins tomorrow, we cannot repeat as champions.
  • If Gonzaga beats Kentucky in the finals, we win.
  • If Kentucky makes it to the finals and loses, the worst we can finish is 4th.
  • If Louisville wins tomorrow, ZachB cannot win.
  • No matter what happens in the games tomorrow, we will still have a scenario to finish top 2.
  • At the end of the Sunday night, we will either be in 6th, 12th, or 14th.
  • We are currently in 13th.
  • 7 of the top 12 teams have no chance to cash.
  • We cannot win if Kentucky wins it all.
  • If Gonzaga beats Duke, we end the night in 14th no matter what happens in the other game.
  • If Louisville and Duke win, we end the night in 6th, but have no chance to finish first.
  • The worst we can finish at the end of the tournament is 18th.  This would happen if Kentucky, Wisconsin, Duke and Louisville made it to the final four and Wisconsin beat Louisville.
  • In 7 of the 32 scenarios remaining, we finish in third, with a remaining 4 scenarios where we finish in fourth.
  • In 24 out of the 32 scenarios we finish in the top 10.
  • Based on current odds, the Final Four is expected to be Kentucky, Wisconsin, Duke, and Michigan State with Kentucky beating Duke in the finals.  In that scenario we finish 7th.

There are 4 possible final four scenarios.  Each has its own heading.  Under each of the 4 scenarios, I list a finals result, and, given that result, who finishes first, second, and what place my team finishes.

Potential Winners with 6 games to play

Final Four: Kentucky, Wisconsin, Duke, Louisville

Kentucky beats Duke: Yosarian, ZachB, 8

Duke beats Kentucky: Juho, Pookie, 3

Kentucky beats Louisville: Yosarian, Bayz, 16

Louisville beats Kentucky: Juho, One Shining MGF, 2

Wisconsin beats Duke: Monte, Wally, 7

Duke beats Wisconsin: Monte, ZachB, 4

Wisconsin beats Louisville: Monte, Wally, 18

Louisville beats Wisconsin: Wally, Monte, 3

Final Four: Kentucky, Wisconsin, Duke, Michigan State

Kentucky beats Duke: Yosarian, ZachB, 7

Duke beats Kentucky: Pookie, Juho, 4

Kentucky beats Michigan St: Yosarian, ZachB, 13

Michigan State beats Kentucky: Juho, One Shining MGF, 2

Wisconsin beats Duke: Monte, ZachB, 6

Duke beats Wisconsin: ZachB, Monte, 4

Wisconsin beats Michigan State: ZachB, Wally, 15

Michigan State beats Wisconsin: Wally, ZachB, 3

Final Four: Kentucky, Wisconsin, Gonzaga, Louisville

Kentucky beats Gonzaga: Yosarian, Lavarel, 5

Gonzaga beats Kentucky: One Shining MGF, Coop, 1

Kentucky beats Louisville: Lavarel, Yosarian, 15

Louisville beats Kentucky: Juho, Wally, 3

Wisconsin beats Gonzaga: Wally, ur1, 6

Gonzaga beats Wisconsin: Wally, One Shining MGF, 2

Wisconsin beats Louisville: Wally, Monte, 16

Louisville beats Wisconsin: Wally, Monte, 4

Final Four: Kentucky, Wisconsin, Gonzaga, Michigan State

Kentucky beats Gonzaga: Lavarel, ZachB, 7

Gonzaga beats Kentucky: One Shining MGF, ZachB, 1

Kentucky beats Michigan State: Lavarel, ZachB, 13

Michigan State beats Kentucky: Yosarian, Juho, 3

Wisconsin beats Gonzaga: Wally, ZachB, 7

Gonzaga beats Wisconsin: ZachB, Wally, 3

Wisconsin beats Michigan State: Wally, Zach B, 15

Michigan State beats Wisconsin: Wally, ZachB, 3