User: rbutler

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rbutler0
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Posts by rbutler

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Comment: C: Deseq metadata bug on repeat runs with parallel
... Even without dependencies It still throws the error for minimum version for S4Vectors and BiocGenerics during compilation, then has issues with Iranges having an array sum error and more. It appears there are some big changes for 3.10? ...
written 5 weeks ago by rbutler0
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Comment: C: Deseq metadata bug on repeat runs with parallel
... That was fun. I installed several github bioconductor packages before realizing I should probably have installed the devel version of Bioconductor in one step. Developer I am not. ``` > library(BiocParallel) > register(MulticoreParam(3)) > library("airway") > data("airway") > ddsSE = ...
written 5 weeks ago by rbutler0
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Deseq metadata bug on repeat runs with parallel
... I have encountered a curious bug that I haven't seen posted yet. When DESeq is rerun multiple times, it seems to multiply the metadata fields by the square of the `MulticoreParam`. By the second or third time it significantly grows the file size and slows the run time, fourth time it errors out. Can ...
deseq2 written 6 weeks ago by rbutler0 • updated 6 weeks ago by Michael Love26k
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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 8 weeks ago by rbutler0 • updated 8 weeks 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 9 weeks 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 9 weeks ago by rbutler0 • updated 9 weeks ago by Michael Love26k
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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 6 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 6 months ago by rbutler0 • updated 6 months ago by Michael Love26k

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