[BioC] limma topTable problem

[Jianping Jin]

Dear BC list:

I tried limma's lmFit and eBayes with my data set which consists 6 RG_U34A 
chips, 3 of them as condition 1 and the other 3 as condition 2. What I did 
was as the following:

> data <- ReadAffy()
> eset <- gcrma(data)
Computing affinities.Done.
Adjusting for optical effect......Done.
Adjusting for non-specific binding......Done.
Normalizing
Calculating Expression
> design <- model.matrix(~ -1+factor(c(1,1,1,2,2,2)))
> colnames(design) <- c("Diff","Prolif")
> fit <- lmFit(eset,design)
> fit2 <- eBayes(fit)
> topTable(fit2,adjust="fdr")
                   ID        M        A        t      P.Value        B
1742 J01435cds#4_s_at 15.69638 15.78457 374.0793 1.514150e-12 22.64603
8022   X14671cds_s_at 14.58179 14.56121 356.7313 1.514150e-12 22.58357
3700   rc_AA849038_at 14.58663 14.47957 344.0524 1.514150e-12 22.53258
5919   rc_AI237836_at 15.01864 14.98568 338.1369 1.514150e-12 22.50706
8209   X57529cds_s_at 14.96041 14.89656 330.1616 1.514150e-12 22.47075
3655 rc_AA818069_f_at 15.04516 15.02714 325.2206 1.514150e-12 22.44709
8219    X58200mRNA_at 14.45639 14.41961 322.4039 1.514150e-12 22.43318
8281     X62145cds_at 13.81953 13.83622 322.0119 1.514150e-12 22.43121
7941      X06423_g_at 15.00450 14.93952 321.4805 1.514150e-12 22.42855
8225  X58465mRNA_g_at 13.19960 13.18034 320.3176 1.514150e-12 22.42267

## I liked to see how many genes with adjusted p-value < 0.05

> dim(fit2)
[1] 8799    2
> table <- topTable(fit2, number=8799, adjust.method="fdr")
> sum(table[,5]<0.05)
[1] 8788

It was unbelievable that 8788 out of 8799 genes are significantly 
expressed. Therefore I tried to look at p-values before eBayes:

> topTable(fit,adjust.method="fdr")
Error in array(x, c(length(x), 1), if (!is.null(names(x))) list(names(x), 
:
        attempt to set an attribute on NULL

I am not familiar with lmFit and eBayes and don't know if it is appropriate 
to make a gene list based on adjusted p-values. Is it B value better?

I'll appreciate anyone who can help me out!

Jianping

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x Jianping Jin Ph.D.            x
x Bioinformatics scientist      x
x Center for bioinformatics     x
x 3133 Bioinformatics Building  x
x CB# 7104                      x
x University of North Carolina  x
x Chapel Hill, NC 27599         x
x Tel: (919)843-6105            x
x Fax: (919)843-3103            x
x E-mail: jjin at email.unc.edu    x
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