Hi Bernd!

Thanks again for your help!
Maybe you did not see it, but I have this line here:

colnames(design) <- c("intercept", "patient1", "patient2", "treatment")

to rename the column names, so the

tt  <- topTable(fitNoAdj, coef= "treatment", adjust="fdr")

command should work :) (unless I misunderstood you)

Thank you :)

Ninni



On Thu, May 8, 2014 at 11:03 AM, Bernd Klaus <bernd.klaus@embl.de> wrote:

> Hi Ninni,
>
> looks good!
>
> However I would suggest removing the
> "clutter" in front of the design matrix column
> names.
>
> The command
>
> tt  <- topTable(fitNoAdj, coef= "treatment", adjust="fdr")
>
> will probably not work since the last column is called
>
> "factor(treatment, levels = c("control", "treatment"))treatment"
>
> and not
>
> "treatment". Another reason to rename the column names of
> the design matrix ...
>
> Best wishes,
>
> Bernd
>
> On Thu,  8 May 2014 01:18:36 -0700 (PDT)
> "Ninni Nahm \[guest\]" <guest@bioconductor.org> wrote:
>
> > Dear all,
> >
> > I made a design matrix according to the limma user guide. However, I
> wanted to check with you, whether it is correct or not. I feel like I made
> a mistake, but I do not know for sure.
> >
> >
> > I have 3 patients and 2 conditions:
> >
> >
> > df <- data.frame(patient = c("p1","p2","p3", "p1","p2","p3"),
> >               treatment = c("control", "control", "control",
> "treatment", "treatment", "treatment")
> >               )
> >
> > df
> >   patient treatment
> > 1      p1   control
> > 2      p2   control
> > 3      p3   control
> > 4      p1 treatment
> > 5      p2 treatment
> > 6      p3 treatment
> >
> >
> > design <-  model.matrix(~factor(patient) + factor(treatment, levels =
> c("control","treatment")), data= df)
> >
> >
> >
> >
> > design
> >   (Intercept) factor(patient)p2 factor(patient)p3
> > 1           1                 0                 0
> > 2           1                 1                 0
> > 3           1                 0                 1
> > 4           1                 0                 0
> > 5           1                 1                 0
> > 6           1                 0                 1
> >   factor(treatment, levels = c("control", "treatment"))treatment
> > 1                                                              0
> > 2                                                              0
> > 3                                                              0
> > 4                                                              1
> > 5                                                              1
> > 6                                                              1
> > attr(,"assign")
> > [1] 0 1 1 2
> > attr(,"contrasts")
> > attr(,"contrasts")$`factor(patient)`
> > [1] "contr.treatment"
> >
> > attr(,"contrasts")$`factor(treatment, levels = c("control",
> "treatment"))`
> > [1] "contr.treatment"
> >
> > colnames(design) <- c("intercept", "patient1", "patient2", "treatment")
> >
> >
> > fit <- lmFit(eset, design)
> > fit <- eBayes(fitNoAdj)
> > tt  <- topTable(fitNoAdj, coef= "treatment", adjust="fdr")
> >
> >
> > Is this correct?
> >
> > Thank you in advance!
> >
> > Ninni
> >
> >
> >
> >  -- output of sessionInfo():
> >
> > > sessionInfo()
> > R version 3.1.0 (2014-04-10)
> > Platform: x86_64-pc-linux-gnu (64-bit)
> >
> > locale:
> >  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
> >  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
> >  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
> >  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
> >  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
> >
> > attached base packages:
> > [1] parallel  stats     graphics  grDevices utils     datasets  methods
> > [8] base
> >
> > other attached packages:
> >  [1] annotate_1.42.0                       pd.hugene.2.0.st_3.8.1
> >  [3] oligo_1.28.0                          Biostrings_2.32.0
> >  [5] XVector_0.4.0                         IRanges_1.22.6
> >  [7] oligoClasses_1.26.0                   RColorBrewer_1.0-5
> >  [9] xtable_1.7-3
>  hugene20sttranscriptcluster.db_2.14.0
> > [11] org.Hs.eg.db_2.14.0                   RSQLite_0.11.4
> > [13] DBI_0.2-7                             AnnotationDbi_1.26.0
> > [15] GenomeInfoDb_1.0.2                    Biobase_2.24.0
> > [17] BiocGenerics_0.10.0                   limma_3.20.1
> >
> > loaded via a namespace (and not attached):
> >  [1] affxparser_1.36.0     affyio_1.32.0         BiocInstaller_1.14.2
> >  [4] bit_1.1-12            codetools_0.2-8       ff_2.2-13
> >  [7] foreach_1.4.2         GenomicRanges_1.16.2  iterators_1.0.7
> > [10] preprocessCore_1.26.0 splines_3.1.0         stats4_3.1.0
> > [13] XML_3.98-1.1          zlibbioc_1.10.0
> >
> > --
> > Sent via the guest posting facility at bioconductor.org.
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor@r-project.org
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> > Search the archives:
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>

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