[BioC] maSigPro error in getting a design matrix
lohith madireddy
lohithreddym at gmail.com
Fri Oct 30 22:41:22 CET 2009
Never mind... I got it. The design matrix was wrongly specified. The
array names should be the row names not as a separate column. I made
the changes necessary and it works now.
Lohith
On Fri, Oct 30, 2009 at 2:15 PM, lohith madireddy
<lohithreddym at gmail.com> wrote:
> Dear Bioconductors,
>
> I have the following design for my experiment. I am trying to use
> maSigPro to assess temporal differential expression across 3
> experimental groups I want to consider (control, vehicle and Var). The
> design matrix is as shown below in the maSigPro format.
>
>
> design
> X Time Replicate Control Vehicle Var
> 1 Veh Day0 A1.CEL 0 1 0 1 0
> 2 Veh Day0 A2.CEL 0 1 0 1 0
> 3 Veh Day0 A4.CEL 0 1 0 1 0
> 4 Veh Day0 A5.CEL 0 1 0 1 0
> 5 Veh Day12 A1.CEL 12 2 0 1 0
> 6 Veh Day12 A2.CEL 12 2 0 1 0
> 7 Veh Day12 A3.CEL 12 2 0 1 0
> 8 Veh Day0 B1.CEL 0 3 0 1 0
> 9 Veh Day0 B3.CEL 0 3 0 1 0
> 10 Veh Day0 B4.CEL 0 3 0 1 0
> 11 Veh Day12 B1.CEL 12 4 0 1 0
> 12 Veh Day12 B2.CEL 12 4 0 1 0
> 13 Veh Day12 B3.CEL 12 4 0 1 0
> 14 Veh Day0 C1.CEL 0 5 0 1 0
> 15 Veh Day0 C2.CEL 0 5 0 1 0
> 16 Veh Day0 C3.CEL 0 5 0 1 0
> 17 Veh Day0 C4.CEL 0 5 0 1 0
> 18 Veh Day0 C5.CEL 0 5 0 1 0
> 19 Veh Day12 C1.CEL 12 6 0 1 0
> 20 Veh Day12 C2.CEL 12 6 0 1 0
> 21 Veh Day12 C3.CEL 12 6 0 1 0
> 22 Day 0 A1.CEL 0 7 0 0 1
> 23 Day 0 A2.CEL 0 7 0 0 1
> 24 Day 0 A3.CEL 0 7 0 0 1
> 25 Day 5 A1.CEL 5 8 0 0 1
> 26 Day 5 A2.CEL 5 8 0 0 1
> 27 Day 5 A3.CEL 5 8 0 0 1
> 28 Day 12 A1.CEL 12 9 0 0 1
> 29 Day 12 A2.CEL 12 9 0 0 1
> 30 Day 12 A3.CEL 12 9 0 0 1
> 31 Day 31 A1.CEL 31 10 0 0 1
> 32 Day 31 A2.CEL 31 10 0 0 1
> 33 Day 31 A3.CEL 31 10 0 0 1
> 34 Day 0 B1.CEL 0 11 0 0 1
> 35 Day 0 B2.CEL 0 11 0 0 1
> 36 Day 0 B3.CEL 0 11 0 0 1
> 37 Day 0 B4.CEL 0 11 0 0 1
> 38 Day 5 B1.CEL 5 12 0 0 1
> 39 Day 5 B2.CEL 5 12 0 0 1
> 40 Day 5 B3.CEL 5 12 0 0 1
> 41 Day 12 B1.CEL 12 13 0 0 1
> 42 Day 12 B2.CEL 12 13 0 0 1
> 43 Day 12 B3.CEL 12 13 0 0 1
> 44 Day 31 B1.CEL 31 14 0 0 1
> 45 Day 31 B2.CEL 31 14 0 0 1
> 46 Day 31 B3.CEL 31 14 0 0 1
> 47 Day 0 C1.CEL 0 15 0 0 1
> 48 Day 0 C2.CEL 0 15 0 0 1
> 49 Day 0 C3.CEL 0 15 0 0 1
> 50 Day 0 C4.CEL 0 15 0 0 1
> 51 Day 5 C1.CEL 5 16 0 0 1
> 52 Day 5 C2.CEL 5 16 0 0 1
> 53 Day 5 C3.CEL 5 16 0 0 1
> 54 Day 12 C1.CEL 12 17 0 0 1
> 55 Day 12 C2.CEL 12 17 0 0 1
> 56 Day 12 C3.CEL 12 17 0 0 1
> 57 Day 31 C1.CEL 31 18 0 0 1
> 58 Day 31 C2.CEL 31 18 0 0 1
> 59 Day 31 C3.CEL 31 18 0 0 1
> 60 Naive A1.CEL 0 19 1 0 0
> 61 Naive A2.CEL 0 19 1 0 0
> 62 Naive A3.CEL 0 19 1 0 0
> 63 Naive B1.CEL 0 20 1 0 0
> 64 Naive B2.CEL 0 20 1 0 0
> 65 Naive C1.CEL 0 21 1 0 0
> 66 Naive C2.CEL 0 21 1 0 0
> 67 Naive C3.CEL 0 21 1 0 0
>
> I am getting an error when I am going to create a maSigPro design
> matrix and the error states
>> design<-make.design.matrix(
> design.init, degree=3)
> Error in Summary.factor(c(47L, 48L, 49L, 50L, 59L, 60L, 61L, 51L, 52L, :
> min not meaningful for factors
>
>> design<-make.design.matrix(design.init)
> Error in Summary.factor(c(47L, 48L, 49L, 50L, 59L, 60L, 61L, 51L, 52L, :
> min not meaningful for factors
>
> Is the error due to not having arrays at all 4 time points for the
> vehicle and Naive? In other words, can maSigPro analyze when the
> number of replicates for each experimental group is different and the
> arrays are not available at all time points (0, 5, 12, 31) for every
> experimental group (Control, Veh, Var)?
> I have 4 time points overall and I am giving 4-1 = 3 as degree for the model.
>
> Please let me know what can be wrong in my analysis.
>
> sessionInfo()
> R version 2.10.0 (2009-10-26)
> i386-pc-mingw32
>
> locale:
> [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United
> States.1252 LC_MONETARY=English_United States.1252
> [4] LC_NUMERIC=C LC_TIME=English_United States.1252
>
> attached base packages:
> [1] tcltk stats graphics grDevices utils datasets
> methods base
>
> other attached packages:
> [1] maSigPro_1.17.5 DynDoc_1.23.1 widgetTools_1.23.1
> genefilter_1.26.4 rgu34acdf_2.5.0 affy_1.23.12 Biobase_2.5.8
>
> loaded via a namespace (and not attached):
> [1] affyio_1.13.5 annotate_1.23.4 AnnotationDbi_1.7.20
> DBI_0.2-4 limma_3.0.3 Mfuzz_2.3.4
> preprocessCore_1.7.9
> [8] RSQLite_0.7-3 splines_2.10.0 survival_2.35-7
> tkWidgets_1.23.2 tools_2.10.0 xtable_1.5-5
>
>
> Thanks in advance!
>
> With Best Regards,
> Lohith
>
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