[BioC] maSigPro questions

[Ana Conesa]

Ingrid,

The reference profile is indicated by the position of that experimental 
group (series) in the edesign object. After the Time and Replicates 
columns you indicate your eexperimetnal groups. The first one is taken 
as reference.
In your case maSigPro gives you lists of genes (see sigs$summary). The 
first one is the genes that change along time for the reference profile 
and the second is the list of genes which change in comparison to the 
reference profile.

I hope this answer your question

Regards

Ana


Ingrid H. G. Østensen wrote:
>
> Hi
>
> Sorry to be asking so detailed questions but I do fully understand 
> this: If the profile does not differentiate form the reference profile 
> how can it be listed changing genes in the venn diagram for the 
> reference profile. Or maybe I have misunderstood what the reference 
> profile is...... I have two times series; control and treated. Is the 
> control the reference profile?
>
> Ingrid
>
>
> Hi Ingrid
>
> ups! this is a typo mistake. It means a flat profile or a profile
> that does not differenciate to the reference profile.
>
> Ana
>
> >
> >
> >
> >---- Mensaje Original ----
> >De: Ingrid.H.G.Ostensen at rr-research.no
> >Para: aconesa at cipf.es
> >Asunto: RE: [BioC] maSigPro questions
> >Fecha: Fri, 19 Oct 2007 11:19:42 +0200
> >
> >>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]]
> >>>
> >>> _______________________________________________
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> >>> Bioconductor at stat.math.ethz.ch
> >>> https://stat.ethz.ch/mailman/listinfo/bioconductor
> >>> Search the archives: http://news.gmane.org/gmane.science.biology.i
> >nformatics.conductor
> >>
> >>
> >>
>
>
>