Timecourse package
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@priscila-grynberg-3196
Last seen 9.6 years ago
Dear BioCs, I'd like to know if it's possible to analyse two-channel microarray data using the timecourse package. I read the pdf, and the examples use Affy data. I'm working with 70-mer oligonucleotide microarray slides. Here is my experimental design: Control X T1 (Biological Replicate 1) T1 X Control (Biological Replicate 1) Control X T1 (Biological Replicate 2) T1 X Control (Biological Replicate 2) Control X T2 (Biological Replicate 1) T2 X Control (Biological Replicate 1) Control X T2 (Biological Replicate 2) T2 X Control (Biological Replicate 2) My control sample is really important for my analysis. -- Priscila Grynberg, B.Sc., M.Sc. Doutoranda em Bioinformática (Bioinformatics D.Sc student) Laboratório de Genética Bioquímica Universidade Federal de Minas Gerais Tel: +55 31 3409-2628 CV: http://lattes.cnpq.br/8808643075395963 [[alternative HTML version deleted]]
Microarray TimeCourse timecourse Microarray TimeCourse timecourse • 1.6k views
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Yu Chuan Tai ▴ 440
@yu-chuan-tai-1534
Last seen 9.6 years ago
Hi Priscila, Am I right that your data have 2 time points, each with a pair of dye- swap experiments? For each biological replicate, was it sampled repeatedly over time? Looks like timecourse can be used, as long as it's of longitudinal design. You can just flip the log2 ratio for Control X T so that you get two replicated vectors of log2 ratios. Best, Yu Chuan On Tue, 17 Feb 2009, Priscila Grynberg wrote: > Dear BioCs, > I'd like to know if it's possible to analyse two-channel microarray data > using the timecourse package. I read the pdf, and the examples use Affy > data. > > I'm working with 70-mer oligonucleotide microarray slides. Here is my > experimental design: > > Control X T1 (Biological Replicate 1) > T1 X Control (Biological Replicate 1) > > Control X T1 (Biological Replicate 2) > T1 X Control (Biological Replicate 2) > > Control X T2 (Biological Replicate 1) > T2 X Control (Biological Replicate 1) > > Control X T2 (Biological Replicate 2) > T2 X Control (Biological Replicate 2) > > My control sample is really important for my analysis. > > > -- > Priscila Grynberg, B.Sc., M.Sc. > Doutoranda em Bioinform??ica (Bioinformatics D.Sc student) > Laborat??io de Gen??ica Bioqu??ica > Universidade Federal de Minas Gerais > Tel: +55 31 3409-2628 > CV: http://lattes.cnpq.br/8808643075395963 > > [[alternative HTML version deleted]] > >
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Dear Yu and BioCs, Yes, I have a longitudinal time course experiment, with 2 independent biological replicates. Each one had their samples extracted in different months, but they were made exactly like the other: 4hs and 24 hs after treatment. I have also two more times to analyse, but for previously results, I'll analyse just the first 2 times. I'm not very good in statistics! I don't know how how to "flip the log2 ratio for Control X T so that you get two replicated vectors of log2 ratios". I'll tell what I have done so far: 1) I used limma and marray to check the quality of the data and to normalize using robustspline method (the best for my data - I tried all of them). Can I use those results as the input for Timecourse package? 2) I believe that I must create a vector to explain my design experiment for limma package. I On Wed, Feb 18, 2009 at 3:42 AM, Yu Chuan Tai <yuchuan@stat.berkeley.edu>wrote: > Hi Priscila, > > Am I right that your data have 2 time points, each with a pair of dye-swap > experiments? For each biological replicate, was it sampled repeatedly over > time? Looks like timecourse can be used, as long as it's of longitudinal > design. You can just flip the log2 ratio for Control X T so that you get two > replicated vectors of log2 ratios. > > Best, > Yu Chuan > > On Tue, 17 Feb 2009, Priscila Grynberg wrote: > > Dear BioCs, >> I'd like to know if it's possible to analyse two-channel microarray data >> using the timecourse package. I read the pdf, and the examples use Affy >> data. >> >> I'm working with 70-mer oligonucleotide microarray slides. Here is my >> experimental design: >> >> Control X T1 (Biological Replicate 1) >> T1 X Control (Biological Replicate 1) >> >> Control X T1 (Biological Replicate 2) >> T1 X Control (Biological Replicate 2) >> >> Control X T2 (Biological Replicate 1) >> T2 X Control (Biological Replicate 1) >> >> Control X T2 (Biological Replicate 2) >> T2 X Control (Biological Replicate 2) >> >> My control sample is really important for my analysis. >> >> >> -- >> Priscila Grynberg, B.Sc., M.Sc. >> Doutoranda em Bioinform??ica (Bioinformatics D.Sc student) >> Laborat??io de Gen??ica Bioqu??ica >> Universidade Federal de Minas Gerais >> Tel: +55 31 3409-2628 >> CV: http://lattes.cnpq.br/8808643075395963 >> >> [[alternative HTML version deleted]] >> >> >> -- Priscila Grynberg, B.Sc., M.Sc. Doutoranda em Bioinformática (Bioinformatics D.Sc student) Laboratório de Genética Bioquímica Universidade Federal de Minas Gerais Tel: +55 31 3409-2628 CV: http://lattes.cnpq.br/8808643075395963 [[alternative HTML version deleted]]
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Sorry, I send the last email unfinished. I'll restart. Dear Yu and BioCs, Yes, I have a longitudinal time course experiment, with 2 independent biological replicates. Each one had their samples extracted in different months, but they were made exactly like the other: 4hs and 24 hs after treatment. I have also two more times to analyse, but for previously results, I'll analyse just the first 2 times. I'm not very good in statistics! I don't know how how to "flip the log2 ratio for Control X T so that you get two replicated vectors of log2 ratios". I'll tell what I have done so far: 1) I used limma and marray to check the quality of the data and to normalize using robustspline method (the best for my data - I tried all of them). Can I use those results as the input for Timecourse package? 2) I believe that I must create a vector to explain my design experiment for limma package. Can you tell me if my vector is correct based on my targets.txt file? SlideNumber Name FileName Cy3 Cy5 Date 0872 N1 Controle_Cy3x4horas_Cy5_RepI_05Fev2009.gpr WT_RepI 4horas_RepI 05/Fev/2009 0873 N2 4horas_Cy3XControle_Cy5_RepI_05Fev2009.gpr 4horas_RepI WT_RepI 05/Fev/2009 0877 N3 Controle_Cy3X4horas_Cy5_RepII_29Jan2009.gpr WT_RepII 4horas_RepII 29/Jan/2009 0880 N4 4horas_Cy5XControle_Cy3_RepII_29Jan2009.gpr 4horas_RepII WT_RepII 29/Jan/2009 0871 N5 Controle_Cy3X24horas_Cy5_RepI_06Fev2009.gpr WT_RepI 24horas_RepI 06/Fev/2009 0876 N6 24horas_Cy3XControle_Cy5_RepI_06Fev2009.gpr 24horas_RepI WT_RepI 06/Fev/2009 0868 N7 Controle_Cy3X24horas_Cy5_RepII_12Fev2009.gpr WT_RepII 24horas_RepII 12/Fev/2009 0869 N8 24horas_Cy3XControle_Cy5_RepII_12Fev2009.gpr 24horas_RepII WT_RepII 12/Fev/2009 design <- c(1, -1, 2, -2, 1, -1, 2, -2)? I'm sorry for all those questions, but I'm completely by myself here! Thanks! Priscila On Wed, Feb 18, 2009 at 8:24 AM, Priscila Grynberg <priscilag@gmail.com>wrote: > Dear Yu and BioCs, > > Yes, I have a longitudinal time course experiment, with 2 independent > biological replicates. Each one had their samples extracted in different > months, but they were made exactly like the other: 4hs and 24 hs after > treatment. I have also two more times to analyse, but for previously > results, I'll analyse just the first 2 times. > > I'm not very good in statistics! I don't know how how to "flip the log2 > ratio for Control X T so that you get two replicated vectors of log2 > ratios". I'll tell what I have done so far: > > 1) I used limma and marray to check the quality of the data and to > normalize using robustspline method (the best for my data - I tried all of > them). Can I use those results as the input for Timecourse package? > > 2) I believe that I must create a vector to explain my design experiment > for limma package. I > > > > On Wed, Feb 18, 2009 at 3:42 AM, Yu Chuan Tai <yuchuan@stat.berkeley.edu>wrote: > >> Hi Priscila, >> >> Am I right that your data have 2 time points, each with a pair of dye-swap >> experiments? For each biological replicate, was it sampled repeatedly over >> time? Looks like timecourse can be used, as long as it's of longitudinal >> design. You can just flip the log2 ratio for Control X T so that you get two >> replicated vectors of log2 ratios. >> >> Best, >> Yu Chuan >> >> On Tue, 17 Feb 2009, Priscila Grynberg wrote: >> >> Dear BioCs, >>> I'd like to know if it's possible to analyse two-channel microarray data >>> using the timecourse package. I read the pdf, and the examples use Affy >>> data. >>> >>> I'm working with 70-mer oligonucleotide microarray slides. Here is my >>> experimental design: >>> >>> Control X T1 (Biological Replicate 1) >>> T1 X Control (Biological Replicate 1) >>> >>> Control X T1 (Biological Replicate 2) >>> T1 X Control (Biological Replicate 2) >>> >>> Control X T2 (Biological Replicate 1) >>> T2 X Control (Biological Replicate 1) >>> >>> Control X T2 (Biological Replicate 2) >>> T2 X Control (Biological Replicate 2) >>> >>> My control sample is really important for my analysis. >>> >>> >>> -- >>> Priscila Grynberg, B.Sc., M.Sc. >>> Doutoranda em Bioinform??ica (Bioinformatics D.Sc student) >>> Laborat??io de Gen??ica Bioqu??ica >>> Universidade Federal de Minas Gerais >>> Tel: +55 31 3409-2628 >>> CV: http://lattes.cnpq.br/8808643075395963 >>> >>> [[alternative HTML version deleted]] >>> >>> >>> > > > -- > Priscila Grynberg, B.Sc., M.Sc. > Doutoranda em Bioinformática (Bioinformatics D.Sc student) > Laboratório de Genética Bioquímica > Universidade Federal de Minas Gerais > Tel: +55 31 3409-2628 > CV: http://lattes.cnpq.br/8808643075395963 > > -- Priscila Grynberg, B.Sc., M.Sc. Doutoranda em Bioinformática (Bioinformatics D.Sc student) Laboratório de Genética Bioquímica Universidade Federal de Minas Gerais Tel: +55 31 3409-2628 CV: http://lattes.cnpq.br/8808643075395963 [[alternative HTML version deleted]]
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Hi Priscila, For limma, I believe there are many experts here who can answer your questions. By "flip?the log2 ratio for Control X T so that you get two replicated vectors of log2 ratios", I mean you take the minus of log2 ratios (i.e. log2(C/T) becomes -log2(C/T)=log2(T/C)) for those Control X T experiments so that all the log2 ratios are treatment to control. Then you can use the two vectors of log2 ratios of treatment to control and apply mb.long() for picking up differentially expressed genes. Best, Yu Chuan On Tue, 17 Feb 2009, Yu Chuan Tai wrote: > Hi Priscila, > > Am I right that your data have 2 time points, each with a pair of dye-swap > experiments? For each biological replicate, was it sampled repeatedly over > time? Looks like timecourse can be used, as long as it's of longitudinal > design. You can just flip the log2 ratio for Control X T so that you get two > replicated vectors of log2 ratios. > > Best, > Yu Chuan > > On Tue, 17 Feb 2009, Priscila Grynberg wrote: > >> Dear BioCs, >> I'd like to know if it's possible to analyse two-channel microarray data >> using the timecourse package. I read the pdf, and the examples use Affy >> data. >> >> I'm working with 70-mer oligonucleotide microarray slides. Here is my >> experimental design: >> >> Control X T1 (Biological Replicate 1) >> T1 X Control (Biological Replicate 1) >> >> Control X T1 (Biological Replicate 2) >> T1 X Control (Biological Replicate 2) >> >> Control X T2 (Biological Replicate 1) >> T2 X Control (Biological Replicate 1) >> >> Control X T2 (Biological Replicate 2) >> T2 X Control (Biological Replicate 2) >> >> My control sample is really important for my analysis. >> >> >> -- >> Priscila Grynberg, B.Sc., M.Sc. >> Doutoranda em Bioinform??ica (Bioinformatics D.Sc student) >> Laborat??io de Gen??ica Bioqu??ica >> Universidade Federal de Minas Gerais >> Tel: +55 31 3409-2628 >> CV: http://lattes.cnpq.br/8808643075395963 >> >> [[alternative HTML version deleted]] >> >> > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >
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Hi Yu, I get it. I believe I still don't know how to creat the input file. Just like the example in the pdf file? Can it read .gpr files? Priscila On Wed, Feb 18, 2009 at 3:22 PM, Yu Chuan Tai <yuchuan@stat.berkeley.edu>wrote: > Hi Priscila, > > For limma, I believe there are many experts here who can answer your > questions. > By "flip the log2 ratio for Control X T so that you get two replicated > vectors of log2 ratios", I mean you take the minus of log2 ratios (i.e. > log2(C/T) becomes -log2(C/T)=log2(T/C)) for those Control X T experiments so > that all the log2 ratios are treatment to control. > Then you can use the two vectors of log2 ratios of treatment to control and > apply mb.long() for picking up differentially expressed genes. > > Best, > Yu Chuan > > On Tue, 17 Feb 2009, Yu Chuan Tai wrote: > > Hi Priscila, >> >> Am I right that your data have 2 time points, each with a pair of dye-swap >> experiments? For each biological replicate, was it sampled repeatedly over >> time? Looks like timecourse can be used, as long as it's of longitudinal >> design. You can just flip the log2 ratio for Control X T so that you get two >> replicated vectors of log2 ratios. >> >> Best, >> Yu Chuan >> >> On Tue, 17 Feb 2009, Priscila Grynberg wrote: >> >> Dear BioCs, >>> I'd like to know if it's possible to analyse two-channel microarray data >>> using the timecourse package. I read the pdf, and the examples use Affy >>> data. >>> >>> I'm working with 70-mer oligonucleotide microarray slides. Here is my >>> experimental design: >>> >>> Control X T1 (Biological Replicate 1) >>> T1 X Control (Biological Replicate 1) >>> >>> Control X T1 (Biological Replicate 2) >>> T1 X Control (Biological Replicate 2) >>> >>> Control X T2 (Biological Replicate 1) >>> T2 X Control (Biological Replicate 1) >>> >>> Control X T2 (Biological Replicate 2) >>> T2 X Control (Biological Replicate 2) >>> >>> My control sample is really important for my analysis. >>> >>> >>> -- >>> Priscila Grynberg, B.Sc., M.Sc. >>> Doutoranda em Bioinform??ica (Bioinformatics D.Sc student) >>> Laborat??io de Gen??ica Bioqu??ica >>> Universidade Federal de Minas Gerais >>> Tel: +55 31 3409-2628 >>> CV: http://lattes.cnpq.br/8808643075395963 >>> >>> [[alternative HTML version deleted]] >>> >>> >>> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > -- Priscila Grynberg, B.Sc., M.Sc. Doutoranda em Bioinformática (Bioinformatics D.Sc student) Laboratório de Genética Bioquímica Universidade Federal de Minas Gerais Tel: +55 31 3409-2628 CV: http://lattes.cnpq.br/8808643075395963 [[alternative HTML version deleted]]
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No, it doesn't take gpr files. As indicated in the help file, it takes "An object of class matrix, MAList, marrayNorm, or exprSet containing log-ratios or log-values of expression for a series of microarrays" These are objects you get after you pre-process your raw data. Best, Yu Chuan On Wed, 18 Feb 2009, Priscila Grynberg wrote: > Hi Yu, > > I get it. I believe I still don't know how to creat the input file. Just > like the example in the pdf file? Can it read .gpr files? > Priscila > > On Wed, Feb 18, 2009 at 3:22 PM, Yu Chuan Tai <yuchuan at="" stat.berkeley.edu="">wrote: > >> Hi Priscila, >> >> For limma, I believe there are many experts here who can answer your >> questions. >> By "flip the log2 ratio for Control X T so that you get two replicated >> vectors of log2 ratios", I mean you take the minus of log2 ratios (i.e. >> log2(C/T) becomes -log2(C/T)=log2(T/C)) for those Control X T experiments so >> that all the log2 ratios are treatment to control. >> Then you can use the two vectors of log2 ratios of treatment to control and >> apply mb.long() for picking up differentially expressed genes. >> >> Best, >> Yu Chuan >> >> On Tue, 17 Feb 2009, Yu Chuan Tai wrote: >> >> Hi Priscila, >>> >>> Am I right that your data have 2 time points, each with a pair of dye-swap >>> experiments? For each biological replicate, was it sampled repeatedly over >>> time? Looks like timecourse can be used, as long as it's of longitudinal >>> design. You can just flip the log2 ratio for Control X T so that you get two >>> replicated vectors of log2 ratios. >>> >>> Best, >>> Yu Chuan >>> >>> On Tue, 17 Feb 2009, Priscila Grynberg wrote: >>> >>> Dear BioCs, >>>> I'd like to know if it's possible to analyse two-channel microarray data >>>> using the timecourse package. I read the pdf, and the examples use Affy >>>> data. >>>> >>>> I'm working with 70-mer oligonucleotide microarray slides. Here is my >>>> experimental design: >>>> >>>> Control X T1 (Biological Replicate 1) >>>> T1 X Control (Biological Replicate 1) >>>> >>>> Control X T1 (Biological Replicate 2) >>>> T1 X Control (Biological Replicate 2) >>>> >>>> Control X T2 (Biological Replicate 1) >>>> T2 X Control (Biological Replicate 1) >>>> >>>> Control X T2 (Biological Replicate 2) >>>> T2 X Control (Biological Replicate 2) >>>> >>>> My control sample is really important for my analysis. >>>> >>>> >>>> -- >>>> Priscila Grynberg, B.Sc., M.Sc. >>>> Doutoranda em Bioinform??ica (Bioinformatics D.Sc student) >>>> Laborat??io de Gen??ica Bioqu??ica >>>> Universidade Federal de Minas Gerais >>>> Tel: +55 31 3409-2628 >>>> CV: http://lattes.cnpq.br/8808643075395963 >>>> >>>> [[alternative HTML version deleted]] >>>> >>>> >>>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at stat.math.ethz.ch >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >> > > > -- > Priscila Grynberg, B.Sc., M.Sc. > Doutoranda em Bioinform?tica (Bioinformatics D.Sc student) > Laborat?rio de Gen?tica Bioqu?mica > Universidade Federal de Minas Gerais > Tel: +55 31 3409-2628 > CV: http://lattes.cnpq.br/8808643075395963 >
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I get it! Now I'm in trouble with mb.long arguments. Would you mind to help me? Just remembering my design: SlideNumber Name FileName Cy3 Cy5 Date 0872 N1 Controle_Cy3x4horas_Cy5_RepI_05Fev2009.gpr WT_RepI 4horas_RepI 05/Fev/2009 0873 N2 4horas_Cy3XControle_Cy5_RepI_05Fev2009.gpr 4horas_RepI WT_RepI 05/Fev/2009 0877 N3 Controle_Cy3X4horas_Cy5_RepII_29Jan2009.gpr WT_RepII 4horas_RepII 29/Jan/2009 0880 N4 4horas_Cy3XControle_Cy5_RepII_29Jan2009.gpr 4horas_RepII WT_RepII 29/Jan/2009 0871 N5 Controle_Cy3X24horas_Cy5_RepI_06Fev2009.gpr WT_RepI 24horas_RepI 06/Fev/2009 0876 N6 24horas_Cy3XControle_Cy5_RepI_06Fev2009.gpr 24horas_RepI WT_RepI 06/Fev/2009 0868 N7 Controle_Cy3X24horas_Cy5_RepII_12Fev2009.gpr WT_RepII 24horas_RepII 12/Fev/2009 0869 N8 24horas_Cy3XControle_Cy5_RepII_12Fev2009.gpr 24horas_RepII WT_RepII 12/Fev/2009 object - OK method - 1D, paired or 2D? I would go for "2D", but maybe is a "paired". type - default times - 2? (Ref X 4hs and Ref X 24hs) reps - I have 2 biological replicates, but I don't think this is what "reps" wants. prior.df - default prior.COV - default prior.eta - default condition.grp - I dpn't know this one rep.grp - This one I need. But how? time.grp - This one I need. But how? one.sample - false? ref - I still don't know! p - default out.t - I'd like to be true tuning - default HotellingT2.only - True Thanks so much! Priscila On Wed, Feb 18, 2009 at 3:38 PM, Yu Chuan Tai <yuchuan@stat.berkeley.edu>wrote: > No, it doesn't take gpr files. As indicated in the help file, it takes > "An object of class matrix, MAList, marrayNorm, or exprSet containing > log-ratios or log-values of expression for a series of microarrays" > > These are objects you get after you pre-process your raw data. Best, > Yu Chuan > > > On Wed, 18 Feb 2009, Priscila Grynberg wrote: > > Hi Yu, >> >> I get it. I believe I still don't know how to creat the input file. Just >> like the example in the pdf file? Can it read .gpr files? >> Priscila >> >> On Wed, Feb 18, 2009 at 3:22 PM, Yu Chuan Tai <yuchuan@stat.berkeley.edu>> >wrote: >> >> Hi Priscila, >>> >>> For limma, I believe there are many experts here who can answer your >>> questions. >>> By "flip the log2 ratio for Control X T so that you get two replicated >>> vectors of log2 ratios", I mean you take the minus of log2 ratios (i.e. >>> log2(C/T) becomes -log2(C/T)=log2(T/C)) for those Control X T experiments >>> so >>> that all the log2 ratios are treatment to control. >>> Then you can use the two vectors of log2 ratios of treatment to control >>> and >>> apply mb.long() for picking up differentially expressed genes. >>> >>> Best, >>> Yu Chuan >>> >>> On Tue, 17 Feb 2009, Yu Chuan Tai wrote: >>> >>> Hi Priscila, >>> >>>> >>>> Am I right that your data have 2 time points, each with a pair of >>>> dye-swap >>>> experiments? For each biological replicate, was it sampled repeatedly >>>> over >>>> time? Looks like timecourse can be used, as long as it's of longitudinal >>>> design. You can just flip the log2 ratio for Control X T so that you get >>>> two >>>> replicated vectors of log2 ratios. >>>> >>>> Best, >>>> Yu Chuan >>>> >>>> On Tue, 17 Feb 2009, Priscila Grynberg wrote: >>>> >>>> Dear BioCs, >>>> >>>>> I'd like to know if it's possible to analyse two-channel microarray >>>>> data >>>>> using the timecourse package. I read the pdf, and the examples use Affy >>>>> data. >>>>> >>>>> I'm working with 70-mer oligonucleotide microarray slides. Here is my >>>>> experimental design: >>>>> >>>>> Control X T1 (Biological Replicate 1) >>>>> T1 X Control (Biological Replicate 1) >>>>> >>>>> Control X T1 (Biological Replicate 2) >>>>> T1 X Control (Biological Replicate 2) >>>>> >>>>> Control X T2 (Biological Replicate 1) >>>>> T2 X Control (Biological Replicate 1) >>>>> >>>>> Control X T2 (Biological Replicate 2) >>>>> T2 X Control (Biological Replicate 2) >>>>> >>>>> My control sample is really important for my analysis. >>>>> >>>>> >>>>> -- >>>>> Priscila Grynberg, B.Sc., M.Sc. >>>>> Doutoranda em Bioinform??ica (Bioinformatics D.Sc student) >>>>> Laborat??io de Gen??ica Bioqu??ica >>>>> Universidade Federal de Minas Gerais >>>>> Tel: +55 31 3409-2628 >>>>> CV: http://lattes.cnpq.br/8808643075395963 >>>>> >>>>> [[alternative HTML version deleted]] >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor@stat.math.ethz.ch >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> Search the archives: >>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>> >>>> >>> >> >> -- >> Priscila Grynberg, B.Sc., M.Sc. >> Doutoranda em Bioinformática (Bioinformatics D.Sc student) >> Laboratório de Genética Bioquímica >> Universidade Federal de Minas Gerais >> Tel: +55 31 3409-2628 >> CV: http://lattes.cnpq.br/8808643075395963 >> > -- Priscila Grynberg, B.Sc., M.Sc. Doutoranda em Bioinformática (Bioinformatics D.Sc student) Laboratório de Genética Bioquímica Universidade Federal de Minas Gerais Tel: +55 31 3409-2628 CV: http://lattes.cnpq.br/8808643075395963 [[alternative HTML version deleted]]
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I'd suggest that you look at the help file and the example codes in the help file first to see how to use mb.long(). Type help(mb.long) Best, Yu Chuan On Wed, 18 Feb 2009, Priscila Grynberg wrote: > I get it! Now I'm in trouble with mb.long arguments. Would you mind to help > me? > Just remembering my design: > > SlideNumber Name FileName Cy3 Cy5 Date > 0872 N1 Controle_Cy3x4horas_Cy5_RepI_05Fev2009.gpr WT_RepI 4horas_RepI > 05/Fev/2009 > 0873 N2 4horas_Cy3XControle_Cy5_RepI_05Fev2009.gpr 4horas_RepI WT_RepI > 05/Fev/2009 > 0877 N3 Controle_Cy3X4horas_Cy5_RepII_29Jan2009.gpr WT_RepII 4horas_RepII > 29/Jan/2009 > 0880 N4 4horas_Cy3XControle_Cy5_RepII_29Jan2009.gpr 4horas_RepII WT_RepII > 29/Jan/2009 > 0871 N5 Controle_Cy3X24horas_Cy5_RepI_06Fev2009.gpr WT_RepI 24horas_RepI > 06/Fev/2009 > 0876 N6 24horas_Cy3XControle_Cy5_RepI_06Fev2009.gpr 24horas_RepI WT_RepI > 06/Fev/2009 > 0868 N7 Controle_Cy3X24horas_Cy5_RepII_12Fev2009.gpr WT_RepII 24horas_RepII > 12/Fev/2009 > 0869 N8 24horas_Cy3XControle_Cy5_RepII_12Fev2009.gpr 24horas_RepII WT_RepII > 12/Fev/2009 > > > > object - OK > method - 1D, paired or 2D? I would go for "2D", but maybe is a "paired". > type - default > times - 2? (Ref X 4hs and Ref X 24hs) > reps - I have 2 biological replicates, but I don't think this is what "reps" > wants. > prior.df - default > prior.COV - default > prior.eta - default > condition.grp - I dpn't know this one > rep.grp - This one I need. But how? > time.grp - This one I need. But how? > one.sample - false? > ref - I still don't know! > p - default > out.t - I'd like to be true > tuning - default > HotellingT2.only - True > > > Thanks so much! > > Priscila > > > On Wed, Feb 18, 2009 at 3:38 PM, Yu Chuan Tai <yuchuan at="" stat.berkeley.edu="">wrote: > >> No, it doesn't take gpr files. As indicated in the help file, it takes >> "An object of class matrix, MAList, marrayNorm, or exprSet containing >> log-ratios or log-values of expression for a series of microarrays" >> >> These are objects you get after you pre-process your raw data. Best, >> Yu Chuan >> >> >> On Wed, 18 Feb 2009, Priscila Grynberg wrote: >> >> Hi Yu, >>> >>> I get it. I believe I still don't know how to creat the input file. Just >>> like the example in the pdf file? Can it read .gpr files? >>> Priscila >>> >>> On Wed, Feb 18, 2009 at 3:22 PM, Yu Chuan Tai <yuchuan at="" stat.berkeley.edu="">>>> wrote: >>> >>> Hi Priscila, >>>> >>>> For limma, I believe there are many experts here who can answer your >>>> questions. >>>> By "flip the log2 ratio for Control X T so that you get two replicated >>>> vectors of log2 ratios", I mean you take the minus of log2 ratios (i.e. >>>> log2(C/T) becomes -log2(C/T)=log2(T/C)) for those Control X T experiments >>>> so >>>> that all the log2 ratios are treatment to control. >>>> Then you can use the two vectors of log2 ratios of treatment to control >>>> and >>>> apply mb.long() for picking up differentially expressed genes. >>>> >>>> Best, >>>> Yu Chuan >>>> >>>> On Tue, 17 Feb 2009, Yu Chuan Tai wrote: >>>> >>>> Hi Priscila, >>>> >>>>> >>>>> Am I right that your data have 2 time points, each with a pair of >>>>> dye-swap >>>>> experiments? For each biological replicate, was it sampled repeatedly >>>>> over >>>>> time? Looks like timecourse can be used, as long as it's of longitudinal >>>>> design. You can just flip the log2 ratio for Control X T so that you get >>>>> two >>>>> replicated vectors of log2 ratios. >>>>> >>>>> Best, >>>>> Yu Chuan >>>>> >>>>> On Tue, 17 Feb 2009, Priscila Grynberg wrote: >>>>> >>>>> Dear BioCs, >>>>> >>>>>> I'd like to know if it's possible to analyse two-channel microarray >>>>>> data >>>>>> using the timecourse package. I read the pdf, and the examples use Affy >>>>>> data. >>>>>> >>>>>> I'm working with 70-mer oligonucleotide microarray slides. Here is my >>>>>> experimental design: >>>>>> >>>>>> Control X T1 (Biological Replicate 1) >>>>>> T1 X Control (Biological Replicate 1) >>>>>> >>>>>> Control X T1 (Biological Replicate 2) >>>>>> T1 X Control (Biological Replicate 2) >>>>>> >>>>>> Control X T2 (Biological Replicate 1) >>>>>> T2 X Control (Biological Replicate 1) >>>>>> >>>>>> Control X T2 (Biological Replicate 2) >>>>>> T2 X Control (Biological Replicate 2) >>>>>> >>>>>> My control sample is really important for my analysis. >>>>>> >>>>>> >>>>>> -- >>>>>> Priscila Grynberg, B.Sc., M.Sc. >>>>>> Doutoranda em Bioinform??ica (Bioinformatics D.Sc student) >>>>>> Laborat??io de Gen??ica Bioqu??ica >>>>>> Universidade Federal de Minas Gerais >>>>>> Tel: +55 31 3409-2628 >>>>>> CV: http://lattes.cnpq.br/8808643075395963 >>>>>> >>>>>> [[alternative HTML version deleted]] >>>>>> >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>> Bioconductor mailing list >>>>> Bioconductor at stat.math.ethz.ch >>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>> Search the archives: >>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>>> >>>>> >>>> >>> >>> -- >>> Priscila Grynberg, B.Sc., M.Sc. >>> Doutoranda em Bioinform?tica (Bioinformatics D.Sc student) >>> Laborat?rio de Gen?tica Bioqu?mica >>> Universidade Federal de Minas Gerais >>> Tel: +55 31 3409-2628 >>> CV: http://lattes.cnpq.br/8808643075395963 >>> >> > > > -- > Priscila Grynberg, B.Sc., M.Sc. > Doutoranda em Bioinform?tica (Bioinformatics D.Sc student) > Laborat?rio de Gen?tica Bioqu?mica > Universidade Federal de Minas Gerais > Tel: +55 31 3409-2628 > CV: http://lattes.cnpq.br/8808643075395963 >
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I already read everything. I understand the arguments in the examples, because it's Affy data. But for two-channel oligo microarray, with dye-swap, it doesn't fit. That's why I need some help. I have 4 slides for each time. But I can't call them A_01, A_02, A_03, A_04 and B_01, B_02, B_03, B_04, because A_01 and A_02 are the dye-swap. They are not independent samples. How can I explain this to the algorithm? I'm a biologist. It's hard to me. But I'll keep trying. Thanks, Priscila [[alternative HTML version deleted]]
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I see. Timecourse doesn't deal with inter-replicate correlations. In that case, you have to assume A_01 and A_02 are independent and you have 4 replicate vectors. Or you can average A_01 and A_02 (after you flip the log ratios of one of them) and you have 2 replicate vectors. Alternatively, you may also consider using limma package, which has a function for dealing with inter- replicate correlations. If you decide to continue with Timecourse, the analysis will be in the same way as Affy, and you can just follow the example codes in the help file. Best, Yu Chuan On Wed, 18 Feb 2009, Priscila Grynberg wrote: > I already read everything. I understand the arguments in the examples, > because it's Affy data. But for two-channel oligo microarray, with dye-swap, > it doesn't fit. That's why I need some help. > I have 4 slides for each time. But I can't call them A_01, A_02, A_03, A_04 > and B_01, B_02, B_03, B_04, because A_01 and A_02 are the dye-swap. They are > not independent samples. How can I explain this to the algorithm? I'm a > biologist. It's hard to me. But I'll keep trying. > > Thanks, > > Priscila >
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