User: glocke01

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glocke010
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Posts by glocke01

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Comment: C: Up and down regulation in LIMMA for microarray dataset
... In general, it's useful to "inspect the raw data".  For example, take one of your most significant DEGs and make a box plot of expression values (raw counts, TPM, voom-normalized) in both conditions; repeat with some non-significant genes for comparison.  Among other things, this will show you if th ...
written 7 months ago by glocke010
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Comment: A: Can I add subject level effect in DESeq2 and pull the correct contrast?
... Here is the solution I found. It seems to work, but please let me know if there's anything I can improve. library(data.table) ## just for rbindlist ## ## mock up the sample info ## sampleInfo <- data.frame(subject=rep(1:10, each=3), time=rep(0:2, 10)) sampleInfo$dose <- as.factor(as.intege ...
written 8 months ago by glocke010
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Comment: C: Can I add subject level effect in DESeq2 and pull the correct contrast?
... First, thanks for your response. Second, I have found the answer to my original question and will post it ASAP. Why collapse time 1 and time 2? There are a few reasons.  The main one is sensitivity; by adding more observations to the post-treatment group, I should be better able to discover differ ...
written 8 months ago by glocke010
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Can I add subject level effect in DESeq2 and pull the correct contrast?
... In my RNA-seq experiment, I have subjects at two doses (high and low) and three time-points (pre-treatment, after treatment 1, after treatment 2).  I want a subject-level baseline to account for subject-to-subject variability. Thus, my design matrix has three columns: dose, time, and subject.  The ...
deseq2 nested design interaction model written 8 months ago by glocke010
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Comment: C: Is ComBat introducing a signal where there is none?
... thanks for writing this up!  very interesting! ...
written 15 months ago by glocke010
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Comment: C: Ensembl release 84 is out!
... running R 3.2.2 with biomart 2.28.0, I get the following > library(biomaRt) > listMarts(host="www.ensembl.org") [1] biomart version <0 rows> (or 0-length row.names) > ens <- useEnsembl(biomart="ensembl") Error in useMart(biomart = biomart, dataset = dataset, host = host, verbose ...
written 18 months ago by glocke010
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Comment: C: BiomaRt workaround when Biomart server closed
... > listMarts(host="www.ensembl.org") Error in `colnames<-`(`*tmp*`, value = c("biomart", "version")) : 'names' attribute [2] must be the same length as the vector [0] This isn't working anymore (as of May 16 2016) edit: see https://support.bioconductor.org/p/82630/ the cause is probably v ...
written 18 months ago by glocke010

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