[BioC] question: fit2$F.p.value

[James W. MacDonald]

Hi Scott,

Mistretta, Toni-Ann wrote:
> 
> 
> Hello,
> 
> 
> I have fit a group means parameterization to my three samples: A, B,
> C (fit1).  I used contrasts.fit to fit my contrasts of interest: B-A,
> and C-A (fit2).  My question: does fit2$F.p.value apply to the
> differences between the three samples A, B, and C (similar to a
> one-way ANOVA) or does it apply to the differences between the two
> contrasts B-A and C-A?  I really need someone to clarify this point
> for me before I go on and select differentially expressed genes.  In
> my case treatments B and C are very similar so this point is almost
> mute.  However, I will be analyzing data sets in the future where
> treatments B and C are very different making my question very
> important.

Well, I was working under the assumption that the F-statistic was the 
'usual' F-stat (MSR/MSE), but apparently I was mistaken. The help page 
for the MArrayLM class states:

'F.stat': 'numeric' vector giving moderated F-statistics for
           testing all contrasts equal to zero

'F.p.value': 'numeric' vector giving p-value corresponding to
           'F.stat'

That's not perfectly clear (all contrasts could be 'all possible 
contrasts', yes?). So a test:

 > library(fibroEset)
 > data(fibroEset)
 > library(limma)
 > design <- model.matrix(~0+pData(fibroEset)[,2])
 > contrast <- matrix(c(-1,1,0))
 > fit <- lmFit(log2(exprs(fibroEset)), design)
 > fit2 <- contrasts.fit(fit, contrast)
 > fit2 <- eBayes(fit2)
 > contrast <- matrix(c(-1,1,0,-1,0,1,0,-1,1), nc=3)
 > fit3 <- contrasts.fit(fit, contrast)
 > fit3 <- eBayes(fit3)
 > cbind(fit2$F,fit3$F)[1:10,]
               [,1]       [,2]
  [1,] 15.118961041  7.7401961
  [2,] 11.105009661 19.8022284
  [3,]  0.007904608  1.4477756
  [4,]  1.748568559  1.3576871
  [5,]  0.187640831  4.1238891
  [6,]  1.633728790  0.8174006
  [7,]  2.116625209  1.7426943
  [8,]  0.208801377  0.5223336
  [9,]  9.813763553 10.9888647
[10,]  0.010995645  0.8344381

Looks like 'all contrasts' means 'all specified contrasts'.

HTH,

Jim



> 
> Scott Ochsner Baylor College of Medicine One Baylor Plaza Houston,
> TX. 77030
> 
> 
> thanks,
> 
> S
> 
> 
> Sent for S. Ochsner by TAM
> 
> [[alternative HTML version deleted]]
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623


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