User: tony.fox2016

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tony.fox201630
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Posts by tony.fox2016

<prev • 7 results • page 1 of 1 • next >
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modeling tissue effect
... Hi all,  Below is the experimental design, in which I would like to compare the treated vs the untreated group. However, the samples were from 2 origins. I wonder if it is possible to include the tissue effect in the comparison. Any suggestion is appreciated! sample condition tissue ...
deseq2 written 3.7 years ago by tony.fox201630
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Comment: C: a naive question about aov() in R
... In the result, group z has a p-value (in the row fz). I am curious if this p-value makes any sense. ...
written 3.8 years ago by tony.fox201630
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a naive question about aov() in R
... Hi all, I found that in R, when applying aov() to 3 or more groups of data, even there is only one observation in some group, aov() still works. I am not sure how it calculate the within-group variance for this group without any replicates, such as the group z in the following code:   x<-rnor ...
R written 3.8 years ago by tony.fox201630 • updated 3.8 years ago by James W. MacDonald52k
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Answer: A: Multiple group analysis
... res2<-results(dds, contrast=c("treatment","T1", "T2"), test="Wald") res3<-results(dds, contrast=c("treatment","T1", "T3"), test="Wald") ...   ...
written 3.8 years ago by tony.fox201630
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Comment: C: DESeq2 ANODEV with 3 sample groups
... Thanks Michael. This is exactly the answer I wanted! ...
written 3.8 years ago by tony.fox201630
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Comment: C: DESeq2 ANODEV with 3 sample groups
... Hi Michael,  it is easy to understand that the LRT p-value is for the comparison of the 3 levels. However, how can we retrieve the p-value for the comparison of condition B vs A?  Thank you! ...
written 3.8 years ago by tony.fox201630
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DESeq2 factors and ANOVA
... Hi, I have a couple of questions about DESeq2: 1) in the DESeq2 workflow, to test the dex treatment effect, the following command was used: dds <- DESeqDataSet(se, design = ~ cell + dex) And I guess the only factor here is "dex" and it might be more straightforward to use: dds <- DESeqDa ...
deseq2 written 3.8 years ago by tony.fox201630 • updated 3.8 years ago by Michael Love26k

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Scholar 3.8 years ago, created an answer that has been accepted. For A: Multiple group analysis

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