User: ariel

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ariel0
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Posts by ariel

<prev • 17 results • page 1 of 2 • next >
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Comment: C: How to extract factor levels of coldata from deseq object?
... I have a plotting routine to which I'm passing `deseq_obj`, and I was hoping I might get the levels in there. Well gollee, it IS a DataFrame. I had tried to extract the levels from the output of `colData` and thought I got an error and a matrix object. But as you said, it really is a DataFrame and h ...
written 5 months ago by ariel0
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How to extract factor levels of coldata from deseq object?
... Suppose I have run deseq like this: ``` my_coldata$varA = factor(mycoldata$varA, levels=c('control', 'case') my_coldata$varB = factor(mycoldata$varB, levels=c(0,1)) dds = DESeqDataSetFromMatrix( countData=my_counts, colData=my_coldata, design=~varA + varB ) deseq_obj = DESeq( d ...
deseq2 factor coldata levels written 5 months ago by ariel0 • updated 5 months ago by Michael Love24k
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Comment: C: NOOB question: How to use contrasts for subgroup analysis in DESeq2?
... Thanks, Micheal! Your reply speed is absolutely stunning. I have made arrangements with a statistician :) I did read the section on interactions, but I wasn't sure if I really have an interaction here. I'm far from an expert in R formulas, but my understanding is that something like `Case:Gender` w ...
written 5 months ago by ariel0
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Comment: C: NOOB question: How to use contrasts for subgroup analysis in DESeq2?
... Hi @Michael--I thought of another way to phrase the question that might be more direct: If I have created a deseq object with design `~CaseString + Gender`, can I still access results for a subset of the data? For instance, can I create a contrast that would be _equivalent to_ **first** subset dat ...
written 5 months ago by ariel0
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Comment: C: NOOB question: How to use contrasts for subgroup analysis in DESeq2?
... Ok. Defying good community practice, I've cross-posted [here](https://stats.stackexchange.com/questions/393924/help-setting-up-a-contrast-in-r-for-deseq2) to see if a stats person can help. ...
written 6 months ago by ariel0
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Comment: C: NOOB question: How to use contrasts for subgroup analysis in DESeq2?
... The problem is, I'm so clueless about contrasts, I don't know how to take the vignette example and put it in practice. For instance, if my design was `~ Case + GeneA + GeneB + GeneA:GeneB`, then to subgroup just `Case=="Case"`, my contrast would be `contrast=c(?,?,?)`. ...
written 6 months ago by ariel0
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Comment: C: Why did I get NA p-values in DESeq with continuous variable?
... Right-O. Sorry I missed that. ...
written 6 months ago by ariel0
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Comment: C: Why did I get NA p-values in DESeq with continuous variable?
... So basically, look for features with small p-values and check to see if they look like outliers? ...
written 6 months ago by ariel0
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Comment: C: NOOB question: How to use contrasts for subgroup analysis in DESeq2?
... Added to post. Is this what you wanted? ...
written 6 months ago by ariel0
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Comment: C: Why did I get NA p-values in DESeq with continuous variable?
... Great! I'll try that. Could I have a quick word of advice on how to interpret my "by eye" examination? ...
written 6 months ago by ariel0

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