[BioC] maSigPro Problems in see.genes

[Ana Conesa]

Hi Marcelo

You should be running the see.genes function as:

 > see.genes(sigs$sig.genes$Time, ...)

or

 > see.genes(sigs$sig.genes$Time2, ...)


etc.

Hope this helps

Ana

Marcelo Laia wrote:
> Dear,
>
> We have a Single Series Time Course and we would like to analyse it on maSigPro.
>
> But we got an error in see.genes:
>
>   
>> see.genes(sigs, design, main = "Exp Prof MI", show.fit = T,
>>     
> + dis = design$dis, cluster.method="kmeans", cluster.data = 1, k = 9)
> Error in edesign[, time.col] : incorrect number of dimensions
>
> sig.genes function is OK.
>
>   
>> sigs <- get.siggenes(tstep, rsq = 0.6, vars = "each")
>> sigs$summary
>>     
>     if (stringsAsFactors) factor(x) else x
> 1                            AD1X1FD8 (1)
> 2                            AD1X1FD8 (2)
> (...)
> 136                          ST3X9BD3 (1)
> 137                          ST3X7DD0 (2)
>
> my design file (degree = 4):
>
>   
>> design
>>     
> $dis
>         Time Time2 Time3 Time4
> Array1     1     1     1     1
> Array2     1     1     1     1
> Array3     1     1     1     1
> Array4     5    25   125   625
> Array5     5    25   125   625
> Array6     5    25   125   625
> Array7     9    81   729  6561
> Array8     9    81   729  6561
> Array9     9    81   729  6561
> Array10   13   169  2197 28561
> Array11   13   169  2197 28561
> Array12   13   169  2197 28561
> Array13   17   289  4913 83521
> Array14   17   289  4913 83521
> Array15   17   289  4913 83521
>
> $groups.vector
> [1] "Group" "Group" "Group" "Group"
>
> $edesign
>         Time Replicates Group
> Array1     1          1     1
> Array2     1          1     1
> Array3     1          1     1
> Array4     5          2     1
> Array5     5          2     1
> Array6     5          2     1
> Array7     9          3     1
> Array8     9          3     1
> Array9     9          3     1
> Array10   13          4     1
> Array11   13          4     1
> Array12   13          4     1
> Array13   17          5     1
> Array14   17          5     1
> Array15   17          5     1
>
>   
>> sessionInfo()
>>     
> R version 2.6.2 (2008-02-08)
> i386-pc-mingw32
>
> locale:
> LC_COLLATE=Portuguese_Brazil.1252;LC_CTYPE=Portuguese_Brazil.1252;LC_MONETARY=Portuguese_Brazil.1252;LC_NUMERIC=C;LC_TIME=Portuguese_Brazil.1252
>
> attached base packages:
> [1] tools     stats     graphics  grDevices utils     datasets
> methods   base
>
> other attached packages:
> [1] maSigPro_1.10.0 Biobase_1.16.3
>   
>
> Could you help me? What I could do wrong?
>
> Thank you very much.
>
>   


-- 
------------------------------------------
Ana Conesa, PhD
Bioinformatics Department
Centro de Investigación Príncipe Felipe
Avda. Autopista Saler, 16
46013 Valencia Spain
http://bioinfo.cipf.es/aconesa