[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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