[BioC] maSigPro and "subscript out of bounds"
andrea.grilli at ior.it
andrea.grilli at ior.it
Fri Jun 3 14:59:33 CEST 2011
Hi Valerie,
problem was exaclty number of observations: I tried with "min.obs"
between 3 to 8 and everything worked fine. Maria José Nueda (who
created the package) also suggested this semplification of my
experimental design:
Time Replicates Transfectant Saos
CD99wt22_g21 21 1 1 0
CD99wt22_g7 7 2 1 0
CD99wt22_g0 0 3 1 0
CD99wt22_g14 14 4 1 0
CD99wt36_g21 21 1 1 0
CD99wt36_g7 7 2 1 0
CD99wt36_g0 0 3 1 0
CD99wt36_g14 14 4 1 0
Saos_g21_1 21 5 0 1
Saos_g7_1 7 6 0 1
Saos_g0_1 0 7 0 1
Saos_g14_1 14 8 0 1
Saos_g21_2 21 5 0 1
Saos_g7_2 7 6 0 1
Saos_g0_2 0 7 0 1
Saos_g14_2 14 8 0 1
I hope this suggestion could be useful for futur users...
Thanks to all for the support,
Andrea
Citando Valerie Obenchain <vobencha at fhcrc.org>:
> 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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Dr. Andrea Grilli
andrea.grilli at ior.it
phone 051/63.66.756
Laboratory of Experimental Oncology
Rizzoli Orthopaedic Institute
Codivilla Putti Research Center
via di Barbiano 1/10
40136 - Bologna - Italy
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