User: rbutler

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rbutler0
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Posts by rbutler

<prev • 5 results • page 1 of 1 • next >
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Handling adjustment variables and surrogate variables in model
... In my dataset, I have a covariate that I wish to correct for `cell` and I also want to incorporate a surrogate variable `SV1` for hidden batch effects. My question is if I pass `cell` as an adjustment variable to `sva`, and generate `SV1`, do I now remove `cell` from my model design? ```R # Generat ...
sva deseq2 written 10 days ago by rbutler0 • updated 10 days ago by James W. MacDonald51k
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Comment: C: Using duplication rate as a covariate
... The vignettes have examples that use 2 SVs. Do you ever use more than 2? using `svaseq` to estimate the number of factors with `num.sv` gets me a very high number. I tried sequentially plotting `SV1`, `SV1+SV2`, `SV1+SV2+SV3`, etc using [cleaned matrices](https://www.biostars.org/p/121489/), but I ...
written 11 days ago by rbutler0
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Using duplication rate as a covariate
... Working with a workflow that uses Fastp -> Salmon -> Deseq2 Is it generally considered good practice to control for Fastp's read duplication rate and/or Salmon's percent mapped (from meta_info.json) when doing a Deseq DE analysis? I have noticed a fair amount of variability across a set of s ...
deseq2 salmon fastp written 12 days ago by rbutler0 • updated 12 days ago by Michael Love25k
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Comment: C: lfc shrinkage two factor experiment
... Thanks! I saw the refactoring and I think I understand it, but I am curious about interpreting the outcome. I can for instance relevel `genotype` on `II` and then it will become a single `coef` term, but then would the `condition effect for this re-leveled genotype II` still be the sum of the `condi ...
written 4 months ago by rbutler0
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lfc shrinkage two factor experiment
... Hello, I am working through the vignettes and examples for DESeq2 `?results`. I had a question(s) regarding lfcshrinkage. Looking at Example 2: ## Example 2: two conditions, two genotypes, with an interaction term dds <- makeExampleDESeqDataSet(n=100,m=12) dds$genotype <- fact ...
deseq2 lfcshrink written 4 months ago by rbutler0 • updated 4 months ago by Michael Love25k

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