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Question: maSigPro error in getting a design matrix
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gravatar for lohith madireddy
8.1 years ago by
lohith madireddy40 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
ADD COMMENTlink modified 8.1 years ago • written 8.1 years ago by lohith madireddy40
0
gravatar for lohith madireddy
8.1 years ago by
lohith madireddy40 wrote:
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 >
ADD COMMENTlink written 8.1 years ago by lohith madireddy40
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