[BioC] How to plot gene on their chromosome?

[Simon Noël]

Whell, now I got the result I wanted.  In R, I use

>library(org.Hs.eg.db)

>mysymbols <- scan("./Gene_list.csv", what = 'character', skip =1)
>myEgIDs <- unlist(mget(mysymbols, org.Hs.egSYMBOL2EG))
>write.table(myEgIDs,file="myEgIDs.xls")

After, I use my .xls with the program stripe.

Thans's you for your help.

Does anyone have an idea about my problem with qc()?


Selon Simon Noël <simon.noel.2 at ulaval.ca>, 23.05.2009:

> I have try your procedure and every thing is loking fine for now.  What's the
> netx step to plot my genes on their chromosomes?
>
> Selon Simon Noël <simon.noel.2 at ulaval.ca>, 21.05.2009:
>
> > I am sorry.  Has I say, I am new to R and bioconductor.  I am still
> learning.
> >
> > I will try this tomorow and I will write you back to tell you the result.
> > Thank's you for your help.  Il it's working, I will only have to wory about
> > my
> > problem with qc()...  Or at least for now.  The summer is really young;)
> > Selon Hervé Pagès <hpages at fhcrc.org>, 21.05.2009:
> >
> > > Hi Simon,
> > >
> > > Not a good idea to start a new thread by replying to a different thread
> > > you started previously. Then it shows up under the previous thread even
> > > if you changed the subject.
> > >
> > > more below...
> > >
> > > Simon Noël wrote:
> > > > Hello every one.  I have a question.  I have a gene list in a .xls like
> > > >
> > > > probeID	Symbol
> > > > 1030431	ACSL1
> > > > 4610431	ACTG2
> > > > 4810575	ADAMTSL2
> > > > 1510750	ADH1C
> > > > 4060519	ADORA1
> > > > 5720523	ADRA2A
> > > > 2810482	AHNAK
> > > > 1260270	AIM2
> > > > 4180768	ALAS2
> > > > ...     ...
> > > >
> > > > I want to plote all of those genes on their chromosome.  How can I do
> > this?
> > >
> > > So first you need to map each gene to its chromosome location.
> > >
> > > You can use one of the org.*.eg.db annotation packages for
> > > this (pick up the one for your organism):
> > >
> > >    http://bioconductor.org/packages/release/data/annotation/
> > >
> > > and use the SYMBOL2EG map to map your gene symbols to their corresponding
> > > Entrez IDs and then the CHRLOC map to map your Entrez IDs to their
> > chromosome
> > > locations.
> > >
> > > Example:
> > >
> > >    library(org.Hs.eg.db)
> > >    mysymbols <- c("ACSL1", "ACTG2", "ADAMTSL2", "ADH1C",
> > >                   "ADORA1", "ADRA2A", "AHNAK", "AIM2", "ALAS2")
> > >    myEgIDs <- unlist(mget(mysymbols, org.Hs.egSYMBOL2EG))
> > >    mylocs <- unname(unlist(mget(myEgIDs, org.Hs.egCHRLOC)))
> > >
> > > One thing to be aware of is that those mappings are not necessarily
> > > one-to-one e.g. the same symbol can be associated with different genes:
> > >
> > >    > flat <- toTable(org.Hs.egSYMBOL2EG)
> > >    > names(flat)
> > >    [1] "gene_id" "symbol"
> > >    > any(duplicated(flat$gene_id))
> > >    [1] FALSE
> > >    > any(duplicated(flat$symbol))
> > >    [1] TRUE
> > >
> > > The same thing happens with the org.Hs.egCHRLOC map (I'm not sure
> > > why we have this though, may be others on the list can explain).
> > >
> > > Anyway this explains why 'mylocs' can have more elements than
> 'mysymbols'.
> > >
> > > Cheers,
> > > H.
> > >
> > > >
> > > > Simon Noël
> > > > VP Externe CADEUL
> > > > Association des étudiants et étudiantes en Biochimie, Bio-
> > > > informatique et Microbiologie de l'Université Laval
> > > > CdeC
> > > >
> > > > _______________________________________________
> > > > Bioconductor mailing list
> > > > Bioconductor at stat.math.ethz.ch
> > > > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > > > Search the archives:
> > > http://news.gmane.org/gmane.science.biology.informatics.conductor
> > >
> > > --
> > > Hervé Pagès
> > >
> > > Program in Computational Biology
> > > Division of Public Health Sciences
> > > Fred Hutchinson Cancer Research Center
> > > 1100 Fairview Ave. N, M2-B876
> > > P.O. Box 19024
> > > Seattle, WA 98109-1024
> > >
> > > E-mail: hpages at fhcrc.org
> > > Phone:  (206) 667-5791
> > > Fax:    (206) 667-1319
> > >
> > >
> >
> >
> > Simon Noël
> > VP Externe CADEUL
> > Association des étudiants et étudiantes en Biochimie, Bio-
> > informatique et Microbiologie de l'Université Laval
> > CdeC
>
>
> Simon Noël
> VP Externe CADEUL
> Association des étudiants et étudiantes en Biochimie, Bio-
> informatique et Microbiologie de l'Université Laval
> CdeC


Simon Noël
VP Externe CADEUL
Association des étudiants et étudiantes en Biochimie, Bio-
informatique et Microbiologie de l'Université Laval
CdeC