[BioC] Limma question: positive M values means upregulated in 'Treated' in this case?

[Jenny Drnevich]

Hi Wonjong,

You should always post your questions back to the list for the archives...

You should read through the help for topTable so you can understand what 
the different arguments will do. In the example code you give, you told it 
to sort by M, which it will do from largest negative value to largest 
positive value; this is why the top 10 genes all have negative M values 
(and they are still all down-regulated in group1).


>I sorted saved the longer list and sorted from largest postive, this
>time all P value was 1.

This doesn't make sense - you should give the code you used instead of a 
description of what you thought you did. My guess is that you are somehow 
sorting the genes with significant positive M values to the bottom of the 
ranking, then not getting these genes due to your number cutoff. To quickly 
check how many significantly (at fdr p <= 0.05) up-regulated genes there 
are, try:

coded.results <- decideTests(fit2)
summary(coded.results)

1's are up-regulated, 0's not significant and -1's down-regulated at fdr 
p=0.05.

Best,
Jenny


>In this case, does negative mean up regulated in group1?
>
> > topTable(fit2, coef=1, adjust="fdr", sort.by="M", number=10)
>                          ID     M    A      t  P.Value adj.P.Val     B
>19736  Pf.13_1.328.0_CDS_at -5.47 6.01  -7.56 6.50e-05  2.00e-02  2.30
>18019       AJ290929.1_s_at -5.32 7.35  -3.89 4.59e-03  2.34e-01 -1.97
>20850       Pf.2.3.0_CDS_at -5.21 6.38  -7.09 1.02e-04  2.67e-02  1.86
>20063 Pf.13_1.84.0_CDS_a_at -5.03 4.54 -22.62 1.51e-08  5.74e-05  8.73
>22101    Pf.7.64.0_CDS_a_at -5.03 4.64 -23.24 1.22e-08  5.74e-05  8.84
>18142      K03509.1_RC_x_at -5.00 5.10  -8.62 2.52e-05  1.01e-02  3.19
>21440      Pf.5.22.0_CDS_at -4.96 4.30 -17.30 1.25e-07  2.42e-04  7.50
>18009       AJ290918.1_s_at -4.89 6.87  -5.19 8.29e-04  9.78e-02 -0.23
>22299     Pf.8.290.0_CDS_at -4.83 6.64 -17.24 1.28e-07  2.42e-04  7.48
>18020       AJ290930.1_s_at -4.74 5.51  -6.81 1.35e-04  3.17e-02  1.58
>
>-----Original Message-----
>From: Jenny Drnevich [mailto:drnevich at uiuc.edu]
>Sent: Thursday, October 05, 2006 8:19 AM
>To: Wonjong Moon; bioconductor at stat.math.ethz.ch
>Subject: Re: [BioC] Limma question: positive M values means upregulated
>in 'Treated' in this case?
>
>Hi Wonjong,
>
>
> >I think positive M values means upregulated in 'Treated' (group1),
> >since I did group1 - group2 'Treated' - 'non-treated'. Is it correct?
>
>Yes. If M is positive, that means group1 > group2, and if M is negative,
>group1 < group2
>
>Cheers,
>Jenny
>
>
>
>
>
> >Or
> >negative M value means upregulated in 'Treated'?
> >
> >library(limma)
> >library(affy)
> >data <- ReadAffy()
> >eset <- rma(data)
> >design <- model.matrix(~ -1+factor(c(1,1,1,1,2,2,2,2)))
> >colnames(design) <- c("group1", "group2") fit <- lmFit(eset, design)
> >contrast.matrix <- makeContrasts(group1-group2, levels=design)
> >fit2 <- contrasts.fit(fit, contrast.matrix)
> >fit2 <- eBayes(fit2)
> >topTable(fit2, coef=1, adjust="fdr", sort.by="M", number=10)
> >
> >
> >
> >
> >Thank you.
> >
> >Wonjong
> >
> > > design
> >   group1 group2
> >1      1      0
> >2      1      0
> >3      1      0
> >4      1      0
> >5      0      1
> >6      0      1
> >7      0      1
> >8      0      1
> >attr(,"assign")
> >[1] 1 1
> >attr(,"contrasts")
> >attr(,"contrasts")$`factor(c(1, 1, 1, 1, 2, 2, 2, 2))` [1]
> >"contr.treatment"
> >
> > >
> >
> >
> >         [[alternative HTML version deleted]]
> >
> >_______________________________________________
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>
>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

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