User: Ben

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Ben0
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Posts by Ben

<prev • 14 results • page 1 of 2 • next >
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Comment: C: Creating contrasts which do not include the reference level in limma, edgeR or D
... Thanks for your answer and help. For me - though - these two questions were not similar. Maybe this wasn't clear enough from my side, so I apologize. The question you are linking was regarding missing coefficients in the design model when using a model with no intercept. The question here was about ...
written 4 months ago by Ben0
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Comment: C: Creating contrasts which do not include the reference level in limma, edgeR or D
... Thanks for your answer and the reference! Unfortunately, the example given in the edgeR document deals with model containing a single factor, not an interaction. Things are getting more complicated (at least from my perspective) with an interaction term. I will look into the option without an inter ...
written 4 months ago by Ben0
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Creating contrasts which do not include the reference level in limma, edgeR or DESeq2
... Hi! This question is regarding the creation of a contrast matrix in limma, edgeR or DESeq2, while analyzing RNA-Seq data. The question is: "How to create contrasts which represent comparisons between two factors which are not the reference level (intercept) using a model which contains an interacti ...
limma edger deseq2 written 4 months ago by Ben0 • updated 4 months ago by James W. MacDonald51k
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Comment: C: Question regarding model matrix in limma.
... Thanks for your swift response! I was assuming that I do make some mistakes in interpreting the model matrix. Your clarification helps! Sorry for the group4:time5 mixup... that was my mistake and you are right, that does not exist in the model matrix. But at the end this is (among other contrasts ...
written 4 months ago by Ben0
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Question regarding model matrix in limma.
... I am following the advice: "If you can't find an answer to your question within one hour - ask someone!" So here I write, my question regarding model matrices in limma or DESeq2. I will copy a reprex first: ``` r # Create data frame with information. groups <- data.frame(group = c(rep(1,6), re ...
limma deseq2 written 4 months ago by Ben0 • updated 4 months ago by James W. MacDonald51k
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Comment: C: Blocking factor in limma/voom vs. variancePartition/dream analysis.
... Thanks for the clarification! That's very helpful. So I will continue using the workflow as described in the vignette by using `voom` > `duplicateCorreltion` > `voom` > `dream`, and providing the blocking factor as a random effect within `dream`. Thanks much! ...
written 4 months ago by Ben0
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Blocking factor in limma/voom vs. variancePartition/dream analysis.
... This is a question which came up recently regarding the RNA-Seq in limma/voom, and limma/voom using the variancePartition function `dream()`. When following the workflow outlined in this document ([dream: Differential expression testing with linear mixed models for repeated measures](https://biocon ...
limma voom variancepartition dream written 4 months ago by Ben0 • updated 6 weeks ago by gabriel.hoffman80
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Comment: C: MDS plotting within the limma/voom workflow
... Ok. Great. Thanks for your final comment. I think that clarifies the differences between the limma/voom and DESeq2 workflow regarding the MDS plotting. Thanks much! ...
written 4 months ago by Ben0
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Comment: C: MDS plotting within the limma/voom workflow
... Thanks for your response! I do understand that MDS plots should be based on "close-to-raw" datasets, meaning before any model fitting is performed. This does not seem to be in contrast to performing MDS plots either on `vst` or `voom` transformed dataset, since both of these functions are applied p ...
written 4 months ago by Ben0
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MDS plotting within the limma/voom workflow
... Hi! This is a question regarding the limma/voom workflow for analyzing RNA-Seq dataset. According to the workflow described in "RNA-seq analysis is easy as 1-2-3 with limma, Glimma and edgeR", MDS plotting is performed on the DGEList object which was passed through the `filterByExpr` and `calcNorm ...
limma deseq2 voom written 4 months ago by Ben0 • updated 4 months ago by Gordon Smyth39k

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