[BioC] Unexpected results using limma with numerical factor

[Paul Boutros]

> -----Original Message-----
> From: Gordon Smyth [mailto:smyth at wehi.edu.au]
> Sent: Thursday, August 26, 2004 3:51 AM
> To: paul.boutros at utoronto.ca
> Cc: BioConductor Mailing List
> Subject: Re: [BioC] Unexpected results using limma with numerical factor

<previous commands snipped>

> > > pData(eset);
> >                                TestScore1
> >RAE230_2_060104_LH_IM07T.CEL         0.58
> >RAE230_2_060104_LH_IM08T.CEL        -2.36
> >RAE230_2_060104_LH_IM09T.CEL       -12.24
> >RAE230_2_060104_LH_IM10T.CEL       -14.84
> >RAE230_2_060204_LH_IM07T.CEL         0.15
> >RAE230_2_060204_LH_IM08T.CEL        -3.23
> >RAE230_2_060204_LH_IM09T.CEL       -11.66
> >RAE230_2_060204_LH_IM10T.CEL       -12.91
> >
> > > design <- model.matrix(~-1 + TestScore1, pData(eset));
>
> Almost certainly you should use
>
> design <- model.matrix(~TestScore1, pData(eset))
>
> i.e., there is no justification for removing the intercept from
> your model.

Ach, that's exactly what it was: thanks Gordon.
Paul
> > > design;
> >                                TestScore1
> >RAE230_2_060104_LH_IM07T.CEL         0.58
> >RAE230_2_060104_LH_IM08T.CEL        -2.36
> >RAE230_2_060104_LH_IM09T.CEL       -12.24
> >RAE230_2_060104_LH_IM10T.CEL       -14.84
> >RAE230_2_060204_LH_IM07T.CEL         0.15
> >RAE230_2_060204_LH_IM08T.CEL        -3.23
> >RAE230_2_060204_LH_IM09T.CEL       -11.66
> >RAE230_2_060204_LH_IM10T.CEL       -12.91
> >attr(,"assign")
> >[1] 1
> > > fit1 <- lmFit(eset, design);
> > > fit3 <- eBayes(fit1);
> >
> >
> >All proceeds well without any error-messages, so I believed I had
> >successfully
> >fit my model.  When I extract the data, however, I get some unexpected
> >results:
> >
> > > topTable(fit3, coef=1, number=20, adjust="fdr");
> >                        ID         M        A         t
> P.Value        B
> >104            1367555_at -1.212175 14.77173 -6.808742
> 3.912627e-07 14.75482
> >105          1367556_s_at -1.203275 14.67175 -6.762709
> 3.912627e-07 14.48816
> >3411           1370862_at -1.185363 14.42457 -6.674599
> 3.912627e-07 13.98156
> >2777           1370228_at -1.184768 14.46704 -6.666414
> 3.912627e-07 13.93475
> >549            1368000_at -1.175866 14.33987 -6.622929
> 3.912627e-07 13.68683
> >2697           1370148_at -1.174858 14.32747 -6.617795
> 3.912627e-07 13.65764
> >837            1368288_at -1.170412 14.25957 -6.596453
> 3.912627e-07 13.53649
> >710          1368161_a_at -1.169621 14.27702 -6.589664
> 3.912627e-07 13.49801
> >420            1367871_at -1.166552 14.09481 -6.588461
> 3.912627e-07 13.49120
> >2558           1370009_at -1.162241 14.18252 -6.552347
> 3.912627e-07 13.28707
> >147            1367598_at -1.161072 14.19550 -6.543620
> 3.912627e-07 13.23787
> >2576         1370027_a_at -1.158955 14.13682 -6.536068
> 3.912627e-07 13.19533
> >1136           1368587_at -1.154447 14.04036 -6.517046
> 3.912627e-07 13.08836
> >196            1367647_at -1.154999 14.07951 -6.516673
> 3.912627e-07 13.08627
> >31081 AFFX-r2-P1-cre-5_at -1.153568 14.05140 -6.510380
> 3.912627e-07 13.05094
> >19150          1387082_at -1.153501 14.05431 -6.509674
> 3.912627e-07 13.04697
> >2898         1370349_a_at -1.153164 14.07047 -6.505935
> 3.912627e-07 13.02599
> >1235           1368686_at -1.152660 14.04966 -6.504796
> 3.912627e-07 13.01960
> >8200           1375651_at -1.152557 14.04428 -6.504674
> 3.912627e-07 13.01892
> >19359          1387291_at -1.151666 14.03699 -6.499744
> 3.912627e-07 12.99127
> >
> >The near-identical M, A, and p-values indicate a problem, and
> none of the
> >genes
> >on this list are very plausible biologically for our test-system.  Based
> >on that
> >I'm pretty sure I've gone astray somewhere.
> >
> >Is it possible to use numeric scores in fitting a linear model with
> >limma?  If
> >so, am I asking the question in the right manner?  If not, are there any
> >BioConductor tools appropriate for this kind of question?
>
> Yes, you can use numeric scores with limma.
>
> Gordon
>
> >Any help very much appreciated,
> >Paul
>