[BioC] limma topTable problem

Jianping Jin jjin at email.unc.edu
Wed Sep 28 22:59:29 CEST 2005


Thanks a lot Jenny for helping me out!
Do you have any idea about the error I got when I tried to get p-value 
after lmFit?

> 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

best regards!

Jianping


--On Wednesday, September 28, 2005 3:24 PM -0500 Jenny Drnevich 
<drnevich at uiuc.edu> wrote:

> Hi Jianping,
>
> I have just been learning how to use limma, and I almost stumbled into
> your problem. Because of the way your design matrix is laid out, you need
> to specify a contrast matrix before running the eBayes function. See page
> 31 in the Limma manual for what to do.
>
> Cheers,
> Jenny
>
>
> At 03:07 PM 9/28/2005, you wrote:
>> 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
>>
>> xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
>> 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
>> xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>
> Jenny Drnevich, Ph.D.
>
> Functional Genomics Bioinformatics Specialist
> W.M. Keck Center for Comparative and Functional Genomics
> Roy J. Carver Biotechnology Center
> University of Illinois, Urbana-Champaign
>
> 330 ERML
> 1201 W. Gregory Dr.
> Urbana, IL 61801
> USA
>
> ph: 217-244-7355
> fax: 217-265-5066
> e-mail: drnevich at uiuc.edu



xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
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
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx



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