User: jshouse

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Posts by jshouse

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Comment: C: DESEQ2 linear model of dose
... Thank you Simon!  I will model this. ...
written 2.9 years ago by jshouse0
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Comment: C: DESEQ2 linear model of dose
... Thank you Simon!  I see my mistake. I had used head(arrange(testdf,padj)) from  testdf<-as.data.frame(results(dds)).  When I just did results(dds) it showed me the answer.  > results(dds) log2 fold change (MAP): DOSE 10 vs 0  Wald test p-value: DOSE 10 vs 0  DataFrame with 2982 rows and 6 co ...
written 2.9 years ago by jshouse0
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Comment: C: DESEQ2 linear model of dose
... There was no contrast. This was just design ~ DOSE as listed above. Followed by results(dds). ...
written 2.9 years ago by jshouse0
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DESEQ2 linear model of dose
... I have a question about a linear models in DESeq2. The experimental design is far from optimal, but I wasn't asked about that part.  The samples consist of 12 controls and 3 treatments with different doses of treatment.  coldataset:                          Treatment Sample.ID DOSE               ...
deseq2 written 2.9 years ago by jshouse0 • updated 2.9 years ago by Simon Anders3.6k
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Comment: C: Complex Contrast in DESeq2
... Got it! Thanks! ...
written 3.1 years ago by jshouse0
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Comment: C: Complex Contrast in DESeq2
... Thanks Michael. That is much easier. What about comparing the second two levels of diet to each other? MCD vs. HFD.  I would need to set a new reference level and re-run ?   Best, john ...
written 3.1 years ago by jshouse0
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Comment: C: Complex Contrast in DESeq2
... ddsfull<-DESeqDataSetFromHTSeqCount(sampleTable = sampleTable, directory = input_dir, design=~condition.Diet*condition.Exposure*condition.Days) ddsfull <- ddsfull[ rowSums(counts(ddsfull)) > 1, ] ddsfull$condition.Exposure<-relevel(dds$condition.Exposure, ref = "Vehicle") ddsfull$condit ...
written 3.1 years ago by jshouse0 • updated 3.1 years ago by Michael Love25k
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Comment: C: Complex Contrast in DESeq2
... Thanks Michael for the prompt helpful response as always. I'm not sure that I want to combine the information from Day1 and Day5 when examining DE changes for Diet and Exposure. I expect quite a different set of genes to be DE from 1 day of treatment vs. 5 days of treatment, so I didn't want to incl ...
written 3.1 years ago by jshouse0
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Complex Contrast in DESeq2
... I have an experimental design with 3 main factor effects. (data = mapped rnaseq counts (raw)) Days of treatment (levels = 1 and 5) Diet (levels of BD, HFD, and MCD) Exposure (levels of Vehicle and PERC) I created a full model where condition.group= concatenation of each of these: dds<-DE ...
deseq2 written 3.1 years ago by jshouse0 • updated 3.1 years ago by Michael Love25k
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Comment: C: DESeq2 subexperiments vs. Whole experiment
... Thank you. It did. I should have read the FAQs first. ...
written 3.2 years ago by jshouse0

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Popular Question 13 months ago, created a question with more than 1,000 views. For DESEQ2 linear model of dose

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