Moderator: Ryan C. Thompson

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Posts by Ryan C. Thompson

<prev • 616 results • page 1 of 62 • next >
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Answer: A: What's the relationship between "design" and "contrasts"?
... A design matrix is simply the matrix representation of the system linear equations that you wish to solve using regression, as described here: https://en.wikipedia.org/wiki/Design_matrix. Each column represents a coefficient, and each row represents a sample. It's possible to represent the same mode ...
written 6 days ago by Ryan C. Thompson5.2k
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Comment: C: Creating design matrix in LIMMA
... With a single common reference, you just need one call to modelMatrix. The multiple calls and concatenation with blockDiag were all to handle the multiple reference pools. As for the subject effects, I'm not sure how to incorporate those into a 2-color design. ...
written 7 days ago by Ryan C. Thompson5.2k
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Comment: C: Creating design matrix in LIMMA
... Ok, then that is an important feature of the experimental design, and you to add a column with that information to your sample table. ...
written 9 days ago by Ryan C. Thompson5.2k
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Comment: C: Creating design matrix in LIMMA
... Oh, I wasn't aware that limma provided such a function. Thanks for the correction! I'll edit it into my answer. ...
written 10 days ago by Ryan C. Thompson5.2k
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Comment: C: Creating design matrix in LIMMA
... I don't think this design is appropriate for a 2-color array with dye swaps. I don't have a lot of experience with dye swaps, but my understanding is that a 2-color array design typically doesn't have an intercept (since every array represents the fold change between 2 samples), and a dye-swap is im ...
written 10 days ago by Ryan C. Thompson5.2k
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Answer: A: Creating design matrix in LIMMA
... Since your two stressors apparently have different reference samples (pool1 and pool2), I think the most straightforward way to implement this is by making a separate design matrix for each stressor and then combining them into a single block-diagonal matrix using Matrix::bdiag (correction: limma al ...
written 10 days ago by Ryan C. Thompson5.2k
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Comment: C: Creating design matrix in LIMMA
... You haven't explained what pool1 and pool2 are. I'm guessing they are all the samples for a given stressor pooled together? Also, you say that your experiment involved 4 subjects per stressor, but you've left out important details. Were the same subjects used for both stressors? Were the same subjec ...
written 10 days ago by Ryan C. Thompson5.2k
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Comment: C: Limma-voom vs limma-trend
... I don't think voom is actually estimating more parameters than eBayes with trend=TRUE. They're both estimating the relationship between abundance and variance by fitting a single lowess/loess curve, so I think that the same number of parameters is being estimated either way. They just differ in how ...
written 15 days ago by Ryan C. Thompson5.2k
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Answer: A: Can we use glmQLFit instead of glmFit and then glmLRT in edgeR
... glmQLFit/glmQLFTest can be used almost anywhere that glmFit/glmLRT can, but it's not going to give you a longer list of significant genes than glmFit/glmLRT. In fact, it's almost certain to do the opposite. Performing a differential expression test with no replicates is a last resort method, and yo ...
written 5 weeks ago by Ryan C. Thompson5.2k
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Comment: C: edgeR: Unusual BCV plot
... The links to your plots seem to be inaccessible. ...
written 5 weeks ago by Ryan C. Thompson5.2k

Latest awards to Ryan C. Thompson

Scholar 9 months ago, created an answer that has been accepted. For A: normalized data by DESeq2 look suspicious
Voter 13 months ago, voted more than 100 times.
Scholar 13 months ago, created an answer that has been accepted. For A: normalized data by DESeq2 look suspicious
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: FDR and padj in deseq and edger
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: FDR and padj in deseq and edger
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: FDR and padj in deseq and edger
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Correct assumptions of using limma moderated t-test
Scholar 15 months ago, created an answer that has been accepted. For A: normalized data by DESeq2 look suspicious
Appreciated 15 months ago, created a post with more than 5 votes. For A: Correct assumptions of using limma moderated t-test
Commentator 15 months ago, created a comment with at least 3 up-votes. For C: How to remove dublicate probesets matching to the same gene, after toptable in o
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: EdgeR Multifactorial design with batch effect-trouble with defining contrasts
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Correct assumptions of using limma moderated t-test
Commentator 15 months ago, created a comment with at least 3 up-votes. For C: pass limma contrast matrix variable
Scholar 15 months ago, created an answer that has been accepted. For A: edgeR (3.10.2) contrast question for experimental factors combined as a group
Scholar 15 months ago, created an answer that has been accepted. For A: ribosome profiling analysis with different dispersions
Scholar 15 months ago, created an answer that has been accepted. For A: Cannot find function treatDGE() in package edgeR?
Scholar 15 months ago, created an answer that has been accepted. For A: Technical and biological replates in BitSeq
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Scholar 17 months ago, created an answer that has been accepted. For A: Cannot find function treatDGE() in package edgeR?
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: EdgeR Multifactorial design with batch effect-trouble with defining contrasts
Commentator 18 months ago, created a comment with at least 3 up-votes. For C: How to remove dublicate probesets matching to the same gene, after toptable in o
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: edgeR (3.10.2) contrast question for experimental factors combined as a group
Scholar 19 months ago, created an answer that has been accepted. For A: Cannot find function treatDGE() in package edgeR?
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