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 days 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 7 days 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 7 days ago by Ben0 • updated 7 days ago by James W. MacDonald50k
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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 12 days 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 12 days ago by Ben0 • updated 12 days ago by James W. MacDonald50k
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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 13 days 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 14 days ago by Ben0 • updated 14 days ago by gabriel.hoffman20
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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 19 days 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 20 days 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 21 days ago by Ben0 • updated 20 days ago by Gordon Smyth37k

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