[BioC] topTable; fold-change and data extraction

Mon Aug 11 00:06:31 CEST 2008

Do not despair.

I think the column you want to look at can be referenced as

etab$logFC

That should pull out the fold changes (log wise) of the probes in etab.

etab$logFC > 0

should create a truth table of all those that are greater than zero.

Now, you can use this truth table to pluck out the rows of etab that  
you want by using this truth table as an index like this

etab[etab$logFC > 0,]

The syntax above says "select the rows that are TRUE"

The comma with nothing  is shorthand for "use all the columns" since  
we didn't specify any particular ones.

Hope this helps.

Tom

On Aug 10, 2008, at 5:44 PM, Wijchers, Patrick wrote:

> Dear all,
>
> Forgive me for asking help for such a basic issue. After following  
> a course
>  on R and microarray analysis, I am determined to get better at it.
>  I believe I am very close to at least doing all the basic gene  
> expression
>  analysis (and hope to get more experienced from there), but I am  
> stuck
>  now at a relatively crucial stage.
>
> My aim is straightforward: to extract sets of upregulated and  
> downregulated
>  genes between two conditions from experimental microarray data  
> obtained
>  with mouse430_2 arrays.
>
> So, I obtained moderated t-stats after rma preprocessing:
>
>> library(limma)
>> design<-model.matrix(~factor(m31_eset$genotype))
>> fit<-lmFit(m31_eset, design)
>> ebayes<-eBayes(fit)
>> etab<-topTable(ebayes, coef=2, number=50, adjust.method="fdr",  
>> p.value=0.05,lfc=0)
>> etab
>                 ID      logFC   AveExpr          t      P.Value     
> adj.P.Val
> 37172   1452877_at -2.1867149 10.604163 -28.094315 4.561519e-10  
> 2.057291e-05
> 17792   1433486_at -1.7610156  8.260051 -25.770171 9.826099e-10  
> 2.215834e-05
> 25554   1441248_at -2.0141624  7.457400 -23.580934 2.159235e-09  
> 3.246122e-05
> 17793   1433487_at -1.5573738  7.662227 -21.945441 4.078449e-09  
> 4.598553e-05
> 14414   1430108_at -1.9558887  5.105592 -18.933815 1.497980e-08  
> 1.288990e-04
> 941   1416610_a_at -1.6156069  8.287563 -18.644676 1.714805e-08  
> 1.288990e-04
> 22672 1438366_x_at -1.6615440  9.385415 -16.024782 6.449002e-08  
> 3.712528e-04
> 31808   1447502_at -1.9017788  6.208795 -15.986360 6.585269e-08  
> 3.712528e-04
> 18573   1434267_at -1.3436798  7.025515 -13.057854 3.789018e-07  
> 1.807532e-03
> 39737   1455442_at -1.4437945  6.134666 -12.972677 4.007742e-07  
> 1.807532e-03
> 13110   1428804_at -1.1810039  4.567535 -12.800456 4.493937e-07  
> 1.842555e-03
> 20345   1436039_at -0.9342354  8.330907 -10.566949 2.282503e-06  
> 8.578598e-03
> 22898   1438592_at -1.5371677  4.240373 -10.361602 2.689797e-06  
> 9.331735e-03
> 27128   1442822_at  0.7779881  6.374739  10.236780 2.976198e-06  
> 9.587823e-03
> 21052   1436746_at  0.7136296  8.349428   9.664449 4.799472e-06  
> 1.443073e-02
> 28394   1444088_at -0.8543858  6.742698  -9.354540 6.279629e-06  
> 1.770110e-02
> 19280   1434974_at  0.6953667  6.055993   9.044643 8.278120e-06  
> 2.077425e-02
> 12901   1428595_at -0.9757636  3.665744  -9.042911 8.291091e-06  
> 2.077425e-02
> 25266   1440960_at  0.8017912  5.218203   8.634198 1.208269e-05  
> 2.868112e-02
> 9419  1425113_x_at -0.8156575  8.968278  -8.348717 1.585442e-05  
> 3.407913e-02
> 20142   1435836_at  0.6078861  7.724573   8.347830 1.586798e-05  
> 3.407913e-02
>              B
> 37172 6.877374
> 17792 6.751444
> 25554 6.602080
> 17793 6.464845
> 14414 6.132030
> 941   6.093091
> 22672 5.663773
> 31808 5.656270
> 18573 4.942105
> 39737 4.916286
> 13110 4.863031
> 20345 4.022656
> 22898 3.928929
> 27128 3.870369
>
> The outcome looks fine, with genes with p-values below 0.05,  
> independent
>  of fold-change (and genes have been confirmed in 'Resolver').
>
> However, I want separate files for probe sets with logFC>0  
> (upregulated)
>  and logFC<0 (downregulated), but the option lfc=0 does not  
> distinguish
>  between positive or negative fold change. I have tried lfc>0 and <0,
>  but the function does not recognise that.
>
> There must be a simple way of obtaining these separate data files,
>   but I have been banging my head over this for the whole weekend now,
>  but cannot see the best solution. I have tried all kinds of things  
> and feel
>  I am really close, but nothing has done the job. I have also searched
>  google and the bioconductor FAQs, but to no avail.
>
> Any help is greatly appreciated, I do not want to give up, and I do  
> not want
>  to go back to 'Resolver' or 'Genespring' (even though they make  
> some things
>  very simple).
>
> Thank you,
>
> Patrick
>
> sessionInfo()
> R version 2.7.1 (2008-06-23)
> x86_64-unknown-linux-gnu
>
> locale:
> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US 
> .UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_N 
> AME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTI 
> FICATION=C
>
> attached base packages:
> [1] splines   tools     stats     graphics  grDevices utils      
> datasets
> [8] methods   base
>
> other attached packages:
> [1] vsn_3.6.0            lattice_0.17-8       genefilter_1.20.0
> [4] survival_2.34-1      affy_1.18.2          preprocessCore_1.2.1
> [7] affyio_1.8.1         Biobase_2.0.1        limma_2.14.5
>
> loaded via a namespace (and not attached):
> [1] annotate_1.18.0     AnnotationDbi_1.2.2 DBI_0.2-4
> [4] grid_2.7.1          RSQLite_0.6-9
>
>
> --
> Patrick Wijchers
> Gene control mechanisms and disease group
> MRC Clinical Sciences Centre
> Imperial College
> Hammersmith Campus
> Du Cane Road
> London W12 0NN
> Phone: +44 (0)20 8383 8317 (lab)
>        +44 (0)20 8383 8500 (office)
> Fax:   +44 (0)20 8383 8306
> Email: patrick.wijchers at csc.mrc.ac.uk
>
>
>
> --
> Patrick Wijchers
> Gene control mechanisms and disease group
> MRC Clinical Sciences Centre
> Imperial College
> Hammersmith Campus
> Du Cane Road
> London W12 0NN
> Phone: +44 (0)20 8383 8317 (lab)
>        +44 (0)20 8383 8500 (office)
> Fax:   +44 (0)20 8383 8306
> Email: patrick.wijchers at csc.mrc.ac.uk
>
>
> 	[[alternative HTML version deleted]]
>
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