[BioC] maSigPro and "subscript out of bounds"

[Valerie Obenchain]

Hi Andrea,

I think your problem is with the min.obs argument. See ?p.vector.

Given the dimensions below, you don't have 20 observations for each gene 
in Data.

Valerie


On 05/30/11 07:34, andrea.grilli at ior.it wrote:
> Hi all,
> I'm performing time series experiment with maSigPro package. When I 
> compute regression fit to find significant genes with "p.vector" 
> function, I receive this output:
> Error: subscript out of bounds
>
> Here you can find a resume of my script:
> library("maSigPro")
> parameters <- as.matrix(read.table("./Parameters.txt", header = TRUE)) 
> # design object
> design <- make.design.matrix (parameters, degree = 3)
> Data <- read.table("./Data_RMAnorm.txt") # expression object
> fit <- p.vector(Data, design, Q = 0.05, MT.adjust = "BH", min.obs = 20)
>> Error: subscript out of bounds
>
> It looks like no right dimension of either design or array objects, 
> but both input files look ok for me.
>
>> parameters
>              Time Replicates Transfectant wt22 wt36 Saos1 Saos2
> CD99wt22_g21   21          1            1    1    0     0     0
> CD99wt22_g7     7          2            1    1    0     0     0
> CD99wt22_g0     0          5            1    1    0     0     0
> CD99wt22_g14   14          5            1    1    0     0     0
> CD99wt36_g21   21          1            1    0    1     0     0
> CD99wt36_g7     7          2            1    0    1     0     0
> CD99wt36_g0     0          6            1    0    1     0     0
> CD99wt36_g14   14          6            1    0    1     0     0
> Saos_g21_1     21          3            0    0    0     1     0
> Saos_g7_1       7          4            0    0    0     1     0
> Saos_g0_1       0          7            0    0    0     1     0
> Saos_g14_1     14          8            0    0    0     1     0
> Saos_g21_2     21          3            0    0    0     0     1
> Saos_g7_2       7          4            0    0    0     0     1
> Saos_g0_2       0          7            0    0    0     0     1
> Saos_g14_2     14          8            0    0    0     0     1
>
>> ncol(parameters)
> [1] 7
>> nrow(parameters)
> [1] 16
>> typeof(parameters)
> [1] "integer
>> str(parameters)
>  int [1:16, 1:7] 21 7 0 14 21 7 0 14 21 7 ...
>  - attr(*, "dimnames")=List of 2
>   ..$ : chr [1:16] "CD99wt22_g21" "CD99wt22_g7" "CD99wt22_g0" 
> "CD99wt22_g14" ...
>   ..$ : chr [1:7] "Time" "Replicates" "Transfectant" "wt22" ...
>> rownames(parameters)
>  [1] "CD99wt22_g21" "CD99wt22_g7"  "CD99wt22_g0"  "CD99wt22_g14" 
> "CD99wt36_g21"
>  [6] "CD99wt36_g7"  "CD99wt36_g0"  "CD99wt36_g14" "Saos_g21_1"   
> "Saos_g7_1"
> [11] "Saos_g0_1"    "Saos_g14_1"   "Saos_g21_2"   "Saos_g7_2"    
> "Saos_g0_2"
> [16] "Saos_g14_2"
>
>
>> head(Data)
>           CD99wt22_g21 CD99wt22_g7 CD99wt22_g0 CD99wt22_g14 CD99wt36_g21
> 1007_s_at     8.700365    9.270211    9.430757     9.538669     8.745657
> 1053_at       9.147460    9.271868    9.313653     9.474059     9.070484
> 117_at        5.525772    5.295018    5.324190     5.616462     5.426015
> 121_at        7.677000    7.969068    7.808228     8.013086     7.710776
> 1255_g_at     3.006305    3.081713    2.978214     2.996469     2.962183
> 1294_at       6.062574    6.479575    6.162924     6.582346     6.189861
>           CD99wt36_g7 CD99wt36_g0 CD99wt36_g14 Saos_g21_1 Saos_g7_1 
> Saos_g0_1
> 1007_s_at    9.467785    9.496628     9.481157   9.103450  9.350170  
> 9.746269
> 1053_at      9.238156    9.558520     9.402085   9.063520  8.932865  
> 9.255722
> 117_at       5.724291    5.123912     5.656858   5.283452  5.438294  
> 5.243948
> 121_at       8.105691    8.089829     8.109542   7.770491  7.984196  
> 7.869393
> 1255_g_at    3.077948    2.986192     2.864020   2.954144  2.876680  
> 2.858667
> 1294_at      6.307993    6.206513     6.688947   6.326808  6.327603  
> 5.995019
>           Saos_g14_1 Saos_g21_2 Saos_g7_2 Saos_g0_2 Saos_g14_2
> 1007_s_at   9.769688   9.107356  9.368514  9.613215   9.808061
> 1053_at     9.475658   9.040339  8.939737  9.228254   9.419188
> 117_at      5.556138   5.203474  5.432353  5.437419   5.546174
> 121_at      8.141229   7.663640  7.873487  7.908378   8.231635
> 1255_g_at   3.064729   2.905118  2.911833  2.959471   3.147845
> 1294_at     6.752825   6.373275  6.308702  6.041707   6.706011
>> ncol(Data)
> [1] 16
>> nrow(Data)
> [1] 54675
>> typeof(Data)
> [1] "list"
>> colnames(Data)
>  [1] "CD99wt22_g21" "CD99wt22_g7"  "CD99wt22_g0"  "CD99wt22_g14" 
> "CD99wt36_g21"
>  [6] "CD99wt36_g7"  "CD99wt36_g0"  "CD99wt36_g14" "Saos_g21_1"   
> "Saos_g7_1"
> [11] "Saos_g0_1"    "Saos_g14_1"   "Saos_g21_2"   "Saos_g7_2"    
> "Saos_g0_2"
> [16] "Saos_g14_2"
>
> Data table comes from previous write.table after import of .CEL files 
> with ReadAffy and RMA normalization (from affymetryx platform 
> HG-U133_Plus_2).
> R version is 2.11.1, instead maSigPro is 1.24.1.
>
> I focus that I'm new to Bioconductor, so I hope problem is clear....
> Any idea about possible solutions??
>
> Thanks in advance,
> Andrea
>
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