User: aziza

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aziza0
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Posts by aziza

<prev • 10 results • page 1 of 1 • next >
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Comment: C: Wald vs LRT: different number of significant genes when testing the same coeffic
... Hi, thank you for your reply Michael. The explanation you gave me is in statistical terms and I gather that, I have the same problem when I speak with statisticians here, I was hoping for someone to orient me more on a biological interpretation.  I was expecting that the genes with sig pvalue obtai ...
written 2.8 years ago by aziza0
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Wald vs LRT: different number of significant genes when testing the same coefficient
... Hi list,  My question is simple: what questions are each of these two tests responding to? (why do i get different results when testing for the same coefficient in the Wald vs LRT test?) The FC is the same, the p-values change because the LRT provides a p-value testing for the null hypothesis that ...
deseq2 wald lrt genes significance written 2.8 years ago by aziza0 • updated 2.8 years ago by Michael Love22k
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Comment: C: pairwise combining factors or multifactor analysis ? (DESeq2)
... ok, that's a great tip, Thank you Michael for your guidance and time. ...
written 2.8 years ago by aziza0
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Answer: A: pairwise combining factors or multifactor analysis ? (DESeq2)
... I am using the LRT function to test if the triple interaction term is significant in the model, so the full model includes the triple interaction whereas the reduced model doesn't. My assumption is that when padj < 0.05, the interaction term is significant (one rejects the null hypothesis that th ...
written 2.8 years ago by aziza0
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Comment: C: pairwise combining factors or multifactor analysis ? (DESeq2)
... I post below for ease of reading ...
written 2.8 years ago by aziza0
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Comment: C: pairwise combining factors or multifactor analysis ? (DESeq2)
... Sorry, what I was asking before is how can I use the step function with DESeq2 results, meaning that I need to include a model name and when I use dds as an object in doesn't work. step(FullModel,direction="backward",test="F") Error in terms.default(object) : no terms component nor attribute ...
written 2.8 years ago by aziza0
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Comment: C: pairwise combining factors or multifactor analysis ? (DESeq2)
... I was editting my question as you responded. sorry because now it looks messy. Thanks again ...
written 2.8 years ago by aziza0
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Comment: C: pairwise combining factors or multifactor analysis ? (DESeq2)
... Hi , Thanks for your guiding, I consulted a statistician and was advised to use a multifactor analysis with all three factors and all possible interactions. He suggested to then remove in a step-wise fashion the insignificant coefficients. He has no experience with RNA-Seq data so now that I came to ...
written 2.8 years ago by aziza0
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Answer: A: pairwise combining factors or multifactor analysis ? (DESeq2)
... But according to the manual "Many users begin to add interaction terms to the design formula, when in fact a much simpler approach would give all the results tables that are desired. [...] combine the factors of interest into a single factor with all combinations of the original factors", according ...
written 2.9 years ago by aziza0
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pairwise combining factors or multifactor analysis ? (DESeq2)
... I have a dataset composed of 2 ecotypes, 2 conditions (control, treatment) and 2 geographic units (24 samples in total). I want to look at which genes are differentially expressed: 1. - between ecotype A and B at control, 2. - between ecotype A and B at treatment 3. - between control and treatment ...
deseq2 multifactor pairwise written 2.9 years ago by aziza0

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