User: sbcn

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sbcn50
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Posts by sbcn

<prev • 11 results • page 1 of 2 • next >
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Comment: C: limma regularization on Ballgown
... Hi Alyssa, I am a bit confused how to go from stringtie estimated expression per transcript to limma via ballgown (I am working with triplicates and trying to do some differential expression analysis at the transcript level; so, as the ballgown documentation advises, I will use limma). In the limm ...
written 10 weeks ago by sbcn50
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Comment: C: DESeq2: interaction term as in limma
... Thank you Simon for the clarification. Then the interaction is indeed what I am looking for. Best,   ...
written 6 months ago by sbcn50
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Comment: C: DESeq2: interaction term as in limma
... Thanks a lot Simon for your prompt answer! It is a lot more clear now to me what each term means. If a gene is differentially expressed in B_ko - B_ctrl but not in A_ko - A_ctrl (change in expression triggered by the KO in cell line B but not in cell line A), it will come out of the interaction an ...
written 6 months ago by sbcn50
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DESeq2: interaction term as in limma
... Hi, In limma's documentation, the interaction term is described as: "The first of these questions relates to the WT.S vs WT.U comparison and the second to Mu.S vs Mu.U . The third relates to the difference of differences, i.e., (Mu.S-Mu.U)-(WT.S-WT.U) , which is called the interaction term." I wan ...
limma deseq deseq2 interaction term written 6 months ago by sbcn50 • updated 6 months ago by Simon Anders3.4k
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Answer: A: ballgown custom models
... Hi Alyssa, It definitely helps a lot, thanks! I understand much better now and was able to run the analysis with more confidence. What I mean by pairs - maybe I shouldn't name it this way - are not exactly technical replicates: different regions in the brain from the same animal were sampled. Eac ...
written 19 months ago by sbcn50
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ballgown custom models
... Dear all, I am using for the first time "ballgown" for differential expression of transcripts (after tophat2 + Stringtie). I do have troubles interpreting the results (although it is not really ballgown specific but rather my confusion regarding complex/custom models). Background: I am working wi ...
linear model model matrix ballgown custom model written 20 months ago by sbcn50
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biomaRt fails for M.musculus annotation, Ensembl version 80
... Hi all, I am using biomaRt to annotate Ensembl IDs, from Mus musculus genome, version 80. As the current version is 81, I am using an archived version, here is how I proceed: # connecting to the right version of Ensembl, this works well: my_mart <- useMart(host="may2015.archive.ensembl.org", ...
biomart ensembl written 2.2 years ago by sbcn50 • updated 2.2 years ago by amonida10
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limma duplicateCorrelation - unbalanced paired design
... Dear all, I have a question regarding duplicateCorrelation when applied to a paired design. I am analyzing 8 arrays (Agilent gene expression): 2 experimental groups A and B, samples are paired with one another: A1 with B1, A2 with B2 etc. Sample B2 has to be dropped because of quality issues, so o ...
probe written 4.0 years ago by sbcn50
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Answer: A: limma: paired + multiple comparisons + technical replication?
... Dear Gordon, Thank you for your answer. The only thing is that I also want to compare all groups (1 to 1, all possibilities), and use the "makeContrasts" command - so as to automate better - and I'm not sure if my way of doing it is correct! Here is my code, which actually works now, but I was wo ...
written 4.1 years ago by sbcn50
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limma: paired + multiple comparisons + technical replication ?
... Dear list, This question might be a bit redundant and I apologize for it, if it is, but I can't find a clear answer to what I'm trying to do. I am working on a set of 12 expression one-channel arrays. My target file is basically as follows: FileName Pairs Groups Sample1 1 Group1 Sample2 ...
limma written 4.1 years ago by sbcn50

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