

Hi

This I already have gotten an answer for by Ana, the last thing I asked about is this:


I am plotting the profiles using the PlotGroups method. I have two groups: control and treated. If a gene is in both groups there are drawn two profile in two different colors (red(controll) and green(treatment)). If the gene is only in the control group only one profile is drawn and it is red. But if the gene is in the treatment group but not in the control group, only one profile is drawn. This profile is also red and the box that tells which color is which group does not change (red = control, green = treatment). Is it something wrong with the way colors are set in the method? It looks to me that the first profile to be drawn are to be red, the next green and so on not considering which group the profile belongs too?

Any comments?


Regards,
Ingrid


 
Hello,

The 0 profile is a flat profile: no changes.

Regards.

María.

----- Original Message ----- 
From: "Ana Conesa" <aconesa@cipf.es>
To: "Maria José Nueda Roldán" <MJ.Nueda@ua.es>; "Ingrid H. G. Østensen"
<Ingrid.H.G.Ostensen@rr-research.no>
Sent: Friday, October 26, 2007 1:02 PM
Subject: Re: [BioC] maSigPro questions


> Ingrid,
>
> I am terribly busy this week, so I am forwarding this request to Maria
> Jose Nueda to answer your question.
>
> My apologizes for this delay
>
> Ana
>
>
> Ingrid H. G. Østensen wrote:
> >
> > Hi
> >
> > It work now. :-)
> >
> > I have one more question: In the user guide the following is written:
> > "groups": This will generate a list of significant genes for each
> > experimental group. The list
> > corresponding to the reference group will contain genes whose
> > expression profile is significantly
> > different from a 0 profile. The lists corresponding to the remaining
> > experimental groups will
> > contain genes whose profiles are different from the reference group.
> >
> > What is this 0 profile?
> >
> > Regards,
> > Ingrid
> >
> >
> >
> > Ingrid
> >
> > Which command did you use to generate sigs?
> > you probably need to run like this..
> >
> > > see.genes(sigs$sig.genes[[1]])
> >
> > Ana
> >
> > Ingrid H. G. ?stensen wrote:
> > > Hi
> > >
> > > I am using the maSigPro package but unfortunately I get an error
> > that I can not find the solution to.
> > >
> > >> see.genes(sigs, edesign = designMa, show.fit = T, dis =
> > designMa$dis, cluster.method = "kmeans", cluster.data = 1, k = 9)
> > > [1] "warning: no rows without missing values or less than 2 rows;
> > impossible to compute heatmap"
> > > [1] "warning: NULL data. No visualization possible"
> > > $cut
> > > NULL
> > >
> > > $cluster.algorithm.used
> > > NULL
> > >
> > > $groups
> > > Control UV
> > > UV_a1_t0 0 1
> > > UV_a1_t30 0 1
> > > UV_a1_t90 0 1
> > > UV_a2_t0 0 1
> > > UV_a2_t30 0 1
> > > UV_a2_t90 0 1
> > > C_a1_t0 1 0
> > > C_a1_t30 1 0
> > > C_a1_t90 1 0
> > > C_a2_t0 1 0
> > > C_a2_t30 1 0
> > > C_a2_t90 1 0
> > >
> > > I have run the procedure with log2 values, linear values, with and
> > without (used impute.knn) missing values but still get the error. Any
> > suggestions?
> > >
> > >> sessionInfo()
> > > R version 2.5.1 (2007-06-27)
> > > i386-pc-mingw32
> > >
> > > locale:
> > > LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United
> > Kingdom.1252;LC_MONETARY=English_United
> > Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252
> > >
> > > attached base packages:
> > > [1] "tcltk" "tools" "stats" "graphics" "grDevices" "utils"
> > "datasets" "methods" "base"
> > >
> > > other attached packages:
> > > EMV marray tkWidgets DynDoc widgetTools maSigPro Biobase xtable
> > impute limma
> > > "1.3.1" "1.14.0" "1.14.0" "1.14.0" "1.12.0" "2.0.1" "1.14.1" "1.5-1"
> > "1.0-5" "2.10.7"
> > >
> > >
> > > Regards,
> > > Ingrid
> > >
> > >
> > > [[alternative HTML version deleted]]
> > >
> > > _______________________________________________
> > > Bioconductor mailing list
> > > Bioconductor@stat.math.ethz.ch
> > > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > > Search the archives:
> > http://news.gmane.org/gmane.science.biology.informatics.conductor
> >
> >



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