User: jshouse

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jshouse0
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Posts by jshouse

<prev • 24 results • page 1 of 3 • next >
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DESeq2 lfcShrink time for analysis
... First, this is a rather large experiment. Roughly 3000 features by 1300 samples. Creating the `dds` object takes 12.5 hours with 20 workers at 3.1 ghz, and resultsNames(dds)  consists of 487 items.  > resultsNames(dds)[1:8] [1] "Intercept" "group_00 ...
deseq2 lfcshrink written 14 months ago by jshouse0 • updated 14 months ago by ellascottgm0
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Comment: C: DESeq2 MA plot look different
... Thanks Michael, I didn't catch that. Sorry for wasting your time. I will look there first next time.   ...
written 18 months ago by jshouse0
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DESeq2 MA plot look different
... In the past, (DESeq2 versions < 1.1.4), MA plots from DESeq2 looked like the following (formatting modified by me, but you get the idea). MA plots since 1.14 look different. Is there any reason to be alarmed at how the distribution of l2fc's is dramatically different in its randomness at low c ...
deseq2 maplot written 18 months ago by jshouse0 • updated 18 months ago by Michael Love23k
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Comment: C: DESEQ2 linear model of dose
... My concern is the coefficient for TreatmentB:dose will use count data from treatmentA: doses 1,2,3. Or to put another way, the model as written will model 6 doses of (0) with 1 dose each of 1,2,3 for both TreatmentA:dose and TreatmentB:dose. This may be ignorance on my part regarding the model matri ...
written 2.5 years ago by jshouse0
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Comment: C: DESEQ2 linear model of dose
... For treatment A, wont that design assign B treatment values to a zero dose? Likewise for B with regard to A. ...
written 2.5 years ago by jshouse0
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Comment: C: DESEQ2 linear model of dose
... Thanks Michael and Simon.  My data are structured as follows, where A and B share the zero dose from V (vehicle).  > coldata <- data.frame(treatment=factor(rep(c("A","B","V"),each=3)), + dose=c(1:3,1:3,0,0,0)) > coldata treatment dose 1 A 1 2 ...
written 2.5 years ago by jshouse0
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Comment: C: DESEQ2 linear model of dose
... Is the full rank error because there exists only 1 dose per non-vehicle treatment?  ...
written 2.5 years ago by jshouse0
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Comment: C: DESEQ2 linear model of dose
... Simon, I am sorry that this is taking so much of your time, and I appreciate you sharing it. Using ~ Treatment ​* logdose returns a full rank error.  I'll try to explain more clearly the experimental design by pasting example below.  These two treatments share the same 12 vehicle controls. On purpos ...
written 2.5 years ago by jshouse0 • updated 2.5 years ago by Michael Love23k
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Comment: C: DESEQ2 linear model of dose
... Simon, I was rearranging the code when I got stuck.  The data are arranged as posted in the first box of the original question. When design ~ Group, this worked fine as I was using contrasts to pull out Treatment from Vehicle comparisons.  The dataset actually has 73 different treatments structured ...
written 2.5 years ago by jshouse0
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Comment: C: DESEQ2 linear model of dose
... Thank you Simon!  I will model this. ...
written 2.5 years ago by jshouse0

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