Data set for comparing statistical tests
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Jorge Miró ▴ 160
@jorge-miro-5469
Last seen 9.6 years ago
Hi everybody, I need to compare Student's t-test and the test implemented in the limma package. Does any body has an idea of how I should do? I guess I need a data set with already known differentially expressed genes (maybe this can be done by specially designing the probesets in the used arrays?) and then compare the results of a t-tests and limma test with the expected differentially expressed genes. Where can I get such a data set? Sorry if the question is a bit stupid but I'm new to microarray analysis and statistics... By the way, should this kind of questions be posted here or should I use another forum? Best regards Jorge
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@benilton-carvalho-1375
Last seen 4.1 years ago
Brazil/Campinas/UNICAMP
check the SpikeIn package... in particular the phenoData slot for the datasets available. b On 31 August 2012 10:58, Jorge Mir? <jorgma86 at="" gmail.com=""> wrote: > Hi everybody, > > I need to compare Student's t-test and the test implemented in the > limma package. Does any body has an idea of how I should do? > > I guess I need a data set with already known differentially expressed > genes (maybe this can be done by specially designing the probesets in > the used arrays?) and then compare the results of a t-tests and limma > test with the expected differentially expressed genes. Where can I get > such a data set? > > Sorry if the question is a bit stupid but I'm new to microarray > analysis and statistics... By the way, should this kind of questions > be posted here or should I use another forum? > > > > Best regards > Jorge > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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Thank you very much for the fast answer. I will take a look at the package Best regards Jorge Mir? On Fri, Aug 31, 2012 at 12:01 PM, Benilton Carvalho <beniltoncarvalho at="" gmail.com=""> wrote: > check the SpikeIn package... in particular the phenoData slot for the > datasets available. b > > On 31 August 2012 10:58, Jorge Mir? <jorgma86 at="" gmail.com=""> wrote: >> Hi everybody, >> >> I need to compare Student's t-test and the test implemented in the >> limma package. Does any body has an idea of how I should do? >> >> I guess I need a data set with already known differentially expressed >> genes (maybe this can be done by specially designing the probesets in >> the used arrays?) and then compare the results of a t-tests and limma >> test with the expected differentially expressed genes. Where can I get >> such a data set? >> >> Sorry if the question is a bit stupid but I'm new to microarray >> analysis and statistics... By the way, should this kind of questions >> be posted here or should I use another forum? >> >> >> >> Best regards >> Jorge >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor
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Hi again, I have been trying to understand how I should go on with the spike in data but in vain. Here are the commands I used: ************ Code ************************* > library(SpikeIn) > data(SpikeIn133) #Checked phenoData as suggested.... > phenoData(SpikeIn133) An object of class "AnnotatedDataFrame" sampleNames: 12_13_02_U133A_Mer_Latin_Square_Expt1_R1 12_13_02_U133A_Mer_Latin_Square_Expt2_R1 ... 12_13_02_U133A_Mer_Latin_Square_Expt14_R3 (42 total) varLabels: 203508_at 204563_at ... AFFX-ThrX-3_at (42 total) varMetadata: labelDescription # ... but I could not see the concentrations for the samples. Is it something else I should do? I tryid with pData too and I could not find any information about the samples concentration. *************************** End of code ******************' I guess the SpikeIn133 is a file with raw intensities so I shoud apply rma on it and then use eg limma to test for differential expression of the genes. Am I right? I read the manual for SpikeIn but I can't see anything about the concentrations for each sample in the data set (http://www.bioconductor.org/packages/2.10/data/experiment/manuals/Spi keIn/man/SpikeIn.pdf) Best regards Jorge On Fri, Aug 31, 2012 at 12:01 PM, Benilton Carvalho <beniltoncarvalho at="" gmail.com=""> wrote: > check the SpikeIn package... in particular the phenoData slot for the > datasets available. b > > On 31 August 2012 10:58, Jorge Mir? <jorgma86 at="" gmail.com=""> wrote: >> Hi everybody, >> >> I need to compare Student's t-test and the test implemented in the >> limma package. Does any body has an idea of how I should do? >> >> I guess I need a data set with already known differentially expressed >> genes (maybe this can be done by specially designing the probesets in >> the used arrays?) and then compare the results of a t-tests and limma >> test with the expected differentially expressed genes. Where can I get >> such a data set? >> >> Sorry if the question is a bit stupid but I'm new to microarray >> analysis and statistics... By the way, should this kind of questions >> be posted here or should I use another forum? >> >> >> >> Best regards >> Jorge >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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Hi Jorge, pData(phenoData(SpikeIn133)) Best, Jim On 8/31/2012 2:12 PM, Jorge Mir? wrote: > Hi again, > > I have been trying to understand how I should go on with the spike in > data but in vain. > Here are the commands I used: > > > ************ Code ************************* >> library(SpikeIn) >> data(SpikeIn133) > #Checked phenoData as suggested.... >> phenoData(SpikeIn133) > An object of class "AnnotatedDataFrame" > sampleNames: 12_13_02_U133A_Mer_Latin_Square_Expt1_R1 > 12_13_02_U133A_Mer_Latin_Square_Expt2_R1 ... > 12_13_02_U133A_Mer_Latin_Square_Expt14_R3 (42 total) > varLabels: 203508_at 204563_at ... AFFX-ThrX-3_at (42 total) > varMetadata: labelDescription > > # ... but I could not see the concentrations for the samples. Is it > something else I should do? I tryid with pData too and I could not > find any information about the samples concentration. > > *************************** End of code ******************' > I guess the SpikeIn133 is a file with raw intensities so I shoud apply > rma on it and then use eg limma to test for differential expression of > the genes. Am I right? > > I read the manual for SpikeIn but I can't see anything about the > concentrations for each sample in the data set > (http://www.bioconductor.org/packages/2.10/data/experiment/manuals/S pikeIn/man/SpikeIn.pdf) > > > Best regards > Jorge > > On Fri, Aug 31, 2012 at 12:01 PM, Benilton Carvalho > <beniltoncarvalho at="" gmail.com=""> wrote: >> check the SpikeIn package... in particular the phenoData slot for the >> datasets available. b >> >> On 31 August 2012 10:58, Jorge Mir?<jorgma86 at="" gmail.com=""> wrote: >>> Hi everybody, >>> >>> I need to compare Student's t-test and the test implemented in the >>> limma package. Does any body has an idea of how I should do? >>> >>> I guess I need a data set with already known differentially expressed >>> genes (maybe this can be done by specially designing the probesets in >>> the used arrays?) and then compare the results of a t-tests and limma >>> test with the expected differentially expressed genes. Where can I get >>> such a data set? >>> >>> Sorry if the question is a bit stupid but I'm new to microarray >>> analysis and statistics... By the way, should this kind of questions >>> be posted here or should I use another forum? >>> >>> >>> >>> Best regards >>> Jorge >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at r-project.org >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099
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