lmfit "No residual degrees of freedom"
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David ▴ 860
@david-3335
Last seen 6.0 years ago
Hello, I'm having problems computing comparisons between different groups (this is not array data and i'm not using limma). Any on what the error must be ? > mydata.eset ExpressionSet (storageMode: lockedEnvironment) assayData: 2754598 features, 3 samples element names: exprs protocolData: none phenoData sampleNames: sampleA sampleB sampleC varLabels: Group Sample varMetadata: labelDescription featureData: none experimentData: use 'experimentData(object)' Annotation: fit <- lmFit(mydata.eset, design) .... contrast.matrix > contrast.matrix group1-group2 group1 1 group2 -1 group3 0 group1-group3 group1 1 group2 0 group3 -1 group2-group3 group1 0 group2 1 group3 -1 fit2 <- contrasts.fit(fit, contrast.matrix) fit2 <- eBayes(fit2) Error in ebayes(fit = fit, proportion = proportion, stdev.coef.lim = stdev.coef.lim) : No residual degrees of freedom in linear model fits thanks, david
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@sean-davis-490
Last seen 12 weeks ago
United States
On Mon, Jan 17, 2011 at 8:09 AM, David martin <vilanew@gmail.com> wrote: > Hello, > I'm having problems computing comparisons between different groups (this is > not array data and i'm not using limma). Any on what the error must be ? > > > mydata.eset > ExpressionSet (storageMode: lockedEnvironment) > assayData: 2754598 features, 3 samples > element names: exprs > protocolData: none > phenoData > sampleNames: sampleA sampleB sampleC > varLabels: Group Sample > varMetadata: labelDescription > featureData: none > experimentData: use 'experimentData(object)' > Annotation: > > > fit <- lmFit(mydata.eset, design) > .... > contrast.matrix > > contrast.matrix > group1-group2 > group1 1 > group2 -1 > group3 0 > group1-group3 > group1 1 > group2 0 > group3 -1 > group2-group3 > group1 0 > group2 1 > group3 -1 > > fit2 <- contrasts.fit(fit, contrast.matrix) > fit2 <- eBayes(fit2) > Error in ebayes(fit = fit, proportion = proportion, stdev.coef.lim = > stdev.coef.lim) : > No residual degrees of freedom in linear model fits > > Hi, David. You have three samples and three conditions. That is not enough samples to perform the tests that you want to perform. Your only recourse here, really, is to make ratios among your three arrays and rank genes based on fold change. Alternatively, you can go run some biological replicates. Sean [[alternative HTML version deleted]]
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Ok thanks. On 01/17/2011 02:25 PM, Sean Davis wrote: > On Mon, Jan 17, 2011 at 8:09 AM, David martin<vilanew at="" gmail.com=""> wrote: > >> Hello, >> I'm having problems computing comparisons between different groups (this is >> not array data and i'm not using limma). Any on what the error must be ? >> >>> mydata.eset >> ExpressionSet (storageMode: lockedEnvironment) >> assayData: 2754598 features, 3 samples >> element names: exprs >> protocolData: none >> phenoData >> sampleNames: sampleA sampleB sampleC >> varLabels: Group Sample >> varMetadata: labelDescription >> featureData: none >> experimentData: use 'experimentData(object)' >> Annotation: >> >> >> fit<- lmFit(mydata.eset, design) >> .... >> contrast.matrix >>> contrast.matrix >> group1-group2 >> group1 1 >> group2 -1 >> group3 0 >> group1-group3 >> group1 1 >> group2 0 >> group3 -1 >> group2-group3 >> group1 0 >> group2 1 >> group3 -1 >> >> fit2<- contrasts.fit(fit, contrast.matrix) >> fit2<- eBayes(fit2) >> Error in ebayes(fit = fit, proportion = proportion, stdev.coef.lim = >> stdev.coef.lim) : >> No residual degrees of freedom in linear model fits >> >> > Hi, David. > > You have three samples and three conditions. That is not enough samples to > perform the tests that you want to perform. Your only recourse here, > really, is to make ratios among your three arrays and rank genes based on > fold change. Alternatively, you can go run some biological replicates. > > Sean > > [[alternative HTML version deleted]] > > _______________________________________________ > 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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