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@rr-research.no
>Para: aconesa@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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>nformatics.conductor
>>
>>
>>




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