User: tony.fox2016
tony.fox2016 • 30
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Posts by tony.fox2016
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... 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 ...
written 3.7 years ago by
tony.fox2016 • 30
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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.fox2016 • 30
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... 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 ...
written 3.8 years ago by
tony.fox2016 • 30
• updated
3.8 years ago by
James W. MacDonald ♦ 52k
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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.fox2016 • 30
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... Thanks Michael. This is exactly the answer I wanted!
...
written 3.8 years ago by
tony.fox2016 • 30
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... 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.fox2016 • 30
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... 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 ...
written 3.8 years ago by
tony.fox2016 • 30
• updated
3.8 years ago by
Michael Love ♦ 26k
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