Dear Gilbert,

thank you so much for your posting. I got really interested in learning how
to use the package GeneAnswers, but still find somewhat challenging to
navigate in R from my gene list to geneanswer. Please see below my sension
info. Any help would be greatly appreciated!

regards,

Marcos B. Pinho
Programa de Engenharia Química - PEQ
Laboratório de Engenharia de Cultivos Celulares- LECC
Universidade Federal do Rio de Janeiro - UFRJ
Instituto Nacional de Câncer - INCA
Rio de Janeiro - Brasil


Welcome to Bioconductor

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  'citation("Biobase")' and for packages 'citation(pkgname)'.

> library(tkWidgets)
Loading required package: widgetTools
Loading required package: tcltk
Loading Tcl/Tk interface ... done
Loading required package: DynDoc
> data=ReadAffy(widget=TRUE)
> library(gcrma)
Loading required package: matchprobes
Loading required package: splines
> eset=gcrma(data)
Adjusting for optical effect....Done.
Computing affinities.Done.
Adjusting for non-specific binding....Done.
Normalizing
Calculating Expression
> library(genefilter)
Loading required package: survival
> library (hgu133plus2.db)
Loading required package: AnnotationDbi
Loading required package: DBI
> esetF = nsFilter (eset, require.entrez=TRUE,remove.dupEntrez=TRUE,
feature.exclude="^AFFX",var.cutof=0.5)$eset
> design = model.matrix(~factor(rep(1:2,each=2)))
> colnames(design)=c("K562", "Lucena")
>  design
  K562 Lucena
1    1      0
2    1      0
3    1      1
4    1      1
attr(,"assign")
[1] 0 1
attr(,"contrasts")
attr(,"contrasts")$`factor(rep(1:2, each = 2))`
[1] "contr.treatment"

> library(limma)
> fit =lmFit (esetF, design)
> fit2=eBayes(fit)
> library(annotate)
Loading required package: xtable

Attaching package: 'xtable'


        The following object(s) are masked from package:widgetTools :

         label

> fit2$genes$Symbol=getSYMBOL(fit2$genes$ID, "hgu133plus2")
> fit2$genes$GeneName <- unlist(mget(fit$genes$ID, hgu133plus2GENENAME))
> fit2$genes$EG <- getEG(fit2$genes$ID, "hgu133plus2")
> topTable(fit2, coef=2)
              ID Symbol
5253   209993_at  ABCB1
3378  1553436_at  MUC19
9828 206488_s_at   CD36
6995 222392_x_at   PERP
8973   210603_at  ARD1B
1412   235683_at  SESN3
7573 216191_s_at   TRD@
4013   202948_at  IL1R1
5302   205934_at  PLCL1
4061 205786_s_at  ITGAM
                                                          GeneName     EG
5253        ATP-binding cassette, sub-family B (MDR/TAP), member 1   5243
3378                                          mucin 19, oligomeric 283463
9828                       CD36 molecule (thrombospondin receptor)    948
6995                                 PERP, TP53 apoptosis effector  64065
8973                                ARD1 homolog B (S. cerevisiae)  84779
1412                                                     sestrin 3 143686
7573                                   T cell receptor delta locus   6964
4013                                interleukin 1 receptor, type I   3554
5302                                        phospholipase C-like 1   5334
4061 integrin, alpha M (complement component 3 receptor 3 subunit)   3684
         logFC  AveExpr         t      P.Value   adj.P.Val        B
5253  8.167898 6.410285  28.41936 1.387084e-06 0.008649451 5.223275
3378  7.512443 6.097913  25.70956 2.249499e-06 0.008649451 4.992571
9828  7.318355 6.081049  22.79634 4.015521e-06 0.008649451 4.678934
6995  6.047929 6.736659  20.28712 7.035669e-06 0.008649451 4.336022
8973  6.088776 5.773605  20.23547 7.122355e-06 0.008649451 4.328102
1412  6.589716 5.620394  20.17661 7.222719e-06 0.008649451 4.319030
7573 -6.153962 5.640399 -19.71517 8.071494e-06 0.008649451 4.246141
4013 -6.231328 5.580407 -19.61010 8.281240e-06 0.008649451 4.229097
5302  5.836512 5.809832  19.53496 8.435274e-06 0.008649451 4.216804
4061 -6.788839 7.957034 -18.03301 1.238036e-05 0.008649451 3.951528


On Thu, Feb 4, 2010 at 4:47 PM, Gilbert Feng <g-feng@northwestern.edu>wrote:

> Hi, Marcos
>
> Please check attached sample pdf file. If that is what you want, you can
> use
> GeneAnswers to do that. The essential input is a genelist with optional
> values, like foldchange, p-value, etc. And GeneAnswers can run enrichment
> test and draw a concept-gene network with a concept-gene cross table, if
> you
> have an expression profile, to show how your genes are potentially
> connected
> to KEGG pathways. You can find examples and codes at
> http://www.bioconductor.org/packages/release/bioc/html/GeneAnswers.html
>
> Also, this attached sample pdf file is interactively generated, which means
> you can adjust the layout for your purpose.
>
> Let me know if you have any question.
>
> Thanks
>
> Gilbert
>
>
> On 2/4/10 9:39 AM, "Marcos Pinho" <pinho.microarray@gmail.com> wrote:
>
> > Dear list,
> >
> > I have search extensively old postings but could not find an easy
> > explanation on how to link my gene list generated after a diferential
> > expression analysis with limma to a kegg pathway analysis. Any help would
> be
> > greatly appreciated. Please keep in mind that I am a molecular biologist
> > that can navigate through R , but it is always a challenge, therefore
> > details and or examples are very helpful!
> >
> > cheers,
>
>
>
>
>


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