User: stwestreich

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Posts by stwestreich

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Comment: C: Need help setting up DESeq2 complex model for multi-dose experiment
... Hi Michael, That makes sense.  What if I treated the dose as binary, using a simple "0" or "1" for whether the individual received a dose?  In that case, I should be able to evaluate for individual-specific changes due to dose. In that instance, would I use: dds <- DESeq(ddsBMO, test="LRT", re ...
written 2.8 years ago by stwestreich0
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Comment: C: Need help setting up DESeq2 complex model for multi-dose experiment
... Hi Michael, Ah, my mistake - in the "fission" example in the linked vignette, the interaction term is looking for strain-specific interactions.  There's no "strain" term in my own data. My colData looks like this: Dose = rep(c(0, 0, 25, 35), times = 6) Individual = rep(c("ind4003", "ind4005", "in ...
written 2.8 years ago by stwestreich0
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Need help setting up DESeq2 complex model for multi-dose experiment
... Hello, I have RNAseq data from a longitudinal study, where six participants provided samples first at 0 dose, then at a low dose (25) of medication, and then at a high dose (35) of the same medication.  There are no massive changes that immediately jump out from the change in dosage, so I want to c ...
dose deseq2 multiple time points written 2.8 years ago by stwestreich0 • updated 2.8 years ago by Michael Love26k
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DESeq erroneously normalizing all values to mean of one specific variable - what's wrong?
... I'm running DESeq2_1.6.3 in R_3.1.2 to compare expression levels between two conditions, with a dozen individuals in each condition.  The basic code looks like this: complete_table <- merge(control_table_trimmed, exp_table_trimmed, by=0, all = TRUE) completeCondition <- data.frame(condition= ...
normalization deseq2 fittype parametric written 3.5 years ago by stwestreich0 • updated 3.5 years ago by Michael Love26k
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Comment: C: DESeq normalization seems to reverse the directionality of log2FoldChange - is t
... Hello Wolfgang, Thank you for the suggestion!  I haven't yet tried looking at a scatterplot with the species in question selected, but I'll attempt that to see how much it shifts in position. Yes, I am aware that DESeq2 works off of actual counts.  I am comparing the FPM matrix results with the no ...
written 3.5 years ago by stwestreich0
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DESeq normalization seems to reverse the directionality of log2FoldChange - is this normal?
... Hello all, I'm a graduate student working on analyzing RNA-Seq data from a microbiome - many different species all found in the same environment.  I used some annotation software and Python to get a list of counts for hits to each organism, within each sample.  Imported these counts into R, created ...
rnaseq normalization deseq2 rna-seq cpm written 3.5 years ago by stwestreich0 • updated 3.5 years ago by Wolfgang Huber13k

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