[BioC] maSigPro questions

[Ana Conesa]

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
> 
> 
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