[BioC] Top 50 Candidate genes: "wrong" pValues and B results!

[Gordon Smyth]

At 05:47 PM 26/07/2004, Adrian Peres wrote:
>Hi all
>I am using Limma GUI to analyze Agilent data and I have some troubles.
>Hereafter I placed a sample of the statistic analysis  that looks very 
>strange to me!
>The pValues are all "1" and I don't understand why? B data are not better 
>neither...
>Can my data be so bad?

You are asking whether there is some rule that every microarray experiment 
must lead to significant differentially expressed genes. The answer is no.

Some suggestions: check that you have the treatments in your targets file 
set up correctly; try the same analysis again without background 
correction; change to "fdr" instead of "holm" multiplicity adjustment; 
check your data quality.

Gordon

>Greetings,
>Adrian
>M       A       t       Pvalue  B
>2.099   9.493   27.16   1       -3.417
>-1.389  11.37   -15.45  1       -3.437
>-1.079  8.683   -15.28  1       -3.438
>-1.073  8.952   -14.28  1       -3.442
>0.944   6.831   12.66   1       -3.451
>-0.8108         8.475   -11.51  1       -3.46
>-0.7985         8.784   -11.39  1       -3.461
>-0.803  12.67   -11.38  1       -3.461
>-0.9375         12.22   -11.13  1       -3.463
>-0.8701         10.24   -10.84  1       -3.466
>-1.383  12.55   -10.63  1       -3.468
>-0.846  9.56    -10.22  1       -3.473
>-0.7271         11.98   -10.1   1       -3.474
>0.977   8.603   9.975   1       -3.476
>-0.7734         9.416   -9.716  1       -3.48
>-0.975  9.89    -9.52   1       -3.482
>-0.6683         7.127   -9.514  1       -3.482
>-0.8116         6.528   -9.493  1       -3.483
>-0.673  8.966   -9.434  1       -3.484
>-0.8475         11.26   -9.125  1       -3.489
>-0.8426         10.43   -9.038  1       -3.49
>-0.7633         8.999   -8.977  1       -3.491
>-0.8202         10.14   -8.804  1       -3.494
>-0.6119         9.076   -8.671  1       -3.497
>-0.7045         9.458   -8.611  1       -3.498
>-0.761  10.07   -8.468  1       -3.501
>-0.9212         10.8    -8.437  1       -3.502
>-1.003  8.465   -8.392  1       -3.502