User: j.baldauf

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j.baldauf0
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Posts by j.baldauf

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Answer: A: How to define contrasts for expression changes over time
... Thanks for your response. If it is just an arithmetic rearrangement, shouldn't there be a "+" somewhere? Irrespectively, my results show the same number of differentially expressed genes for both contrasts, so in total 203 genes show expression changes over development between the 2 genotypes. But ...
written 9 months ago by j.baldauf0
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How to define contrasts for expression changes over time
... Hi again, I have an RNA-seq experiment with samples of different genotypes and 3 different developmental stages. For each sample I determined a "genostage" factor genotype <- rep(c("WT","Geno1","Geno2",<other genotypes>), each = 12) dev <- rep(c("stage1","stage2", <other stages>) ...
limma written 9 months ago by j.baldauf0
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Answer: A: Limma: Defining the design matrix of a linear mixed model
... Hi again, I was wondering, how I would define the contrast to determine changes in expression over time between two genotypes. According to examples in the limma manual, I would define the contrast like that: (genostageG1_stageII-genostageG1_stageI)-(genostageG2_stageII-genostageG2_stageI) But th ...
written 9 months ago by j.baldauf0
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Answer: A: Limma: Defining the design matrix of a linear mixed model
... when I include the blocking factor, I obtain different numbers of differentially expressed genes in comparison to not including the blocking factor? I merged the flowcell and lane factors as you suggested into one blocking factor. genostageG1_stageI-genostageG2_stageI with blocking -1               ...
written 9 months ago by j.baldauf0
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Comment: C: Limma: Defining the design matrix of a linear mixed model
... Thanks James and Aaron for your help and recommendations :) To test weather there are any correlations between my samples processed on the same lane, how would I correctly define the blocking factor feeding to duplicateCorrelation? What I tried is the following: I defined in addition to the geno ...
written 9 months ago by j.baldauf0
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Limma: Defining the design matrix of a linear mixed model
... Dear all, I hope to get some elp in setting up my factors and the model matrix to determine differentially expressed genes. I have a RNA-seq data set with samples of 13 genotypes and 3 developmental stages and of each sample, I have 4 biological replicates (in total 180 RNA-seq samples or columns i ...
rnaseq limma differential expression written 9 months ago by j.baldauf0
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Answer: A: workflow.R in BioC 3.3
... I just observed the same error message. Do you already know when this problem will be fixed?  ...
written 17 months ago by j.baldauf0

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