User: fr

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fr150
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Posts by fr

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Benchmarking DESeq / EdgeR / LIMMA vs Lasso vs RF
... Hi! I'm wondering if anyone is aware of any benchmarking between approaches traditionally used in RNAseq or microarray analysis (e.g. DESeq2 / EdgeR / LIMMA) against others such as Random Forest or Lasso regression to identify genes / transcripts that are differentially expressed between conditions ...
lasso limma deseq edger rf written 22 days ago by fr150
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Comment: C: Limma contrasts and design: should it be split based on time points?
... Perfect, thanks a lot for all the clarifications, I really appreciate it ...
written 24 days ago by fr150
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Comment: C: Limma contrasts and design: should it be split based on time points?
... @ATpoint, I do agree with you, but am nevertheless concerned about the FDR. Let's say that you do want to tell this story in 2 parts: first focusing on day 1, and then on day 2. For the first situation, you will be penalizing P-values by the large number of tests included in day 2 as well. ...well, ...
written 24 days ago by fr150
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Comment: C: Limma contrasts matrix drops columns and considers them as reference column
... From which package does that come from? And taking the example of the vignette for instance, how would you do that? ...
written 25 days ago by fr150
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Limma contrasts matrix drops columns and considers them as reference column
... In the [limma vignette](https://www.bioconductor.org/packages/devel/bioc/vignettes/limma/inst/doc/usersguide.pdf) page 44, a simple 2 factorial example is given. My case follows something similar, where I have treatment and time. TS <- paste(targets$Strain, targets$Treatment, sep=".") TS ...
design limma written 26 days ago by fr150 • updated 26 days ago by Luiz30
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Limma contrasts and design: should it be split based on time points?
... I have an experiment that has 2 groups to compare (treated vs control), and for each group I have 12 time points, with 7 patients per time point/group. I am wondering what is the best way to approach the following questions: - Does treatment have an effect? If so, at which time point? - Are there s ...
design limma written 27 days ago by fr150
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Comment: C: R design on 2-way interaction not displaying all options
... Yes, I am aware of this, this is not what I'm asking. I'm asking is how to express all contrasts that are not present? makeContrasts gives everything with reference to the first alphabetical group, so no `treatmentdrug` will show up for the interactions if I take any of your options. I understand t ...
written 9 weeks ago by fr150
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R design on 2-way interaction not displaying all options
... I have a design given by treatment and categorical stages, each with 5 replicates that I want to model in limma, that looks like this: treatment stage 1 ctrl A 2 ctrl B 3 ctrl C 4 ctrl D 1 ...
modeling design limma edger deseq written 9 weeks ago by fr150
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Comment: C: limma fold change problem
... (~4 years after.... sorry!) Where does it say that limma assumes `log2` transformation? ...
written 10 weeks ago by fr150
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Comment: C: RNAseq: should I trim both 3' and 5'?
... Thanks, found this thanks to your comment: https://emea.support.illumina.com/bulletins/2016/04/adapter-trimming-why-are-adapter-sequences-trimmed-from-only-the--ends-of-reads.html ...
written 5 months ago by fr150

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