On Fri, 24 Jun 2011, Christian M. Probst wrote: > Many thanks, Dr. Gordon. > I have run the analysis as suggested. > > Two small questions: > > a) I would like to understand deeply the coef option, besides what is > described in the glmLRT help. Is there a place to look for it? Options to functions are described on the help page for that function so, no, there is not somewhere else to look. > b) If I want to plot the adjusted count values that were used for the GLM > fit and LR analysis, where can I find the equivalent of $pseudo.alt for the > CR analysis? I suppose fitted.values is not the correct answer, as its sums > are not "library size equal". glmFit doesn't use adjusted counts. It uses the original counts that you input. Best wishes Gordon > Thanks in advance. > > Christian > On Wed, Jun 22, 2011 at 9:16 PM, Gordon K Smyth <smyth at="" wehi.edu.au=""> wrote: > >> Dear Christian, >> >> limma syntax doesn't always work in edgeR. We will work to make them as >> analogous as we can, but generalized linear models in edgeR bring in a few >> unavoidable complications into edgeR that are not present in limma. >> >> At the moment, the contrast argument to glmLRT() must be a vector, not a >> matrix, as is explained on the help page for that function. In future we >> will add the matrix capability, but for now you will need to perform >> F-test-like likelihood ratio tests using the coef argument instead. This >> means that you must paramatrize your design matrix so that it contains an >> intercept column: >> >> design <- model.matrix(~group) >> >> Then later you can use >> >> glmLRT(..., coef=2:4) >> >> and so on. This will do the combined test that you want on 3 df for >> differences between the 4 groups. >> >> Best wishes >> Gordon >> >> Date: Mon, 20 Jun 2011 11:12:39 -0300 >>> From: "Christian M. Probst" <cprobst at="" fiocruz.br=""> >>> To: bioconductor at r-project.org >>> Subject: [BioC] EdgeR: ANOVA-like analysis >>> >>> Dear list, >>> >>> I am using edgeR to analyze a RNA-Seq dataset consisting of 4 samples >>> (groups), each with 5 biological replicates. >>> >>> I have read in the Limma manual, as it has an extensive description of >>> design models. In section 8.6, there is a description for multiple groups >>> test, and I have tried to follow the steps there. But the edgeR objects >>> are >>> distinct from the Limma, so I am stucked. >>> >>> Shortly, I want to use edgeR to identify differential expression in all >>> pair-wise comparisons of the 4 groups, as well as combine all pair-wise >>> comparisons into one F-test. >>> >>> I have used the following construction: >>> >>> deF<-glmLRT(dgecRNAF,glmFit(**dgecRNAF, mmcRNA, >>> dispersion=dgecRNAF$common.**dispersion), contrast=contrast.matrix) >>> >>> where dgecRNAF is my DGEList object, mmcRNA is my model matrix, and >>> contrast.matrix is: >>> >>> contrast.matrix >>>> >>> Contrasts >>> Levels A-B A-C A-D B-C B-D C-D >>> A 1 1 1 0 0 0 >>> B -1 0 0 1 1 0 >>> C 0 -1 0 -1 0 1 >>> D 0 0 -1 0 -1 -1 >>> >>> >>> Thanks in advance, >>> >>> -- >>> Dr. Christian Macagnan Probst >>> >>> Adjunct Researcher in Public Health >>> Bioinformatics and Computational Biology Laboratory >>> Functional Genomics Laboratory >>> >>> Carlos Chagas Institute - ICC/FIOCRUZ >>> Curitiba - PR - Brasil >>> >>> Reseacher ID: http://www.researcherid.com/**rid/B-8678-2009<http: www.researcherid.com="" rid="" b-8678-2009=""> >>> >> >> ______________________________**______________________________**___ _______ >> The information in this email is confidential and intended solely for the >> addressee. >> You must not disclose, forward, print or use it without the permission of >> the sender. >> ______________________________**______________________________**___ _______ >> >> -- >> Esta mensagem foi verificada pelo sistema de antiv?rus e >> acredita-se estar livre de perigo. >> > > > > -- > Dr. Christian Macagnan Probst > > Adjunct Researcher in Public Health > Bioinformatics and Computational Biology Laboratory > Functional Genomics Laboratory > > Carlos Chagas Institute - ICC/FIOCRUZ > Curitiba - PR - Brasil > > Reseacher ID: http://www.researcherid.com/rid/B-8678-2009 > Curriculum Lattes: http://lattes.cnpq.br/9371475697752743 >