User: ariel

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ariel0
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Posts by ariel

<prev • 24 results • page 1 of 3 • next >
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Comment: C: Still lots of NA adjusted p-values in DESeq2 after eliminating Cook's distance c
... Thanks! I did not know about the independent filtering setting. ...
written 11 days ago by ariel0
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Comment: C: Still lots of NA adjusted p-values in DESeq2 after eliminating Cook's distance c
... Thanks! I did not know about the independent filtering setting. ...
written 11 days ago by ariel0
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Still lots of NA adjusted p-values in DESeq2 after eliminating Cook's distance cutoff.
... I am using DESeq2 to look for differential abundance in a set of KEGG pathways. It's a downstream analysis of 16s data. I know DESeq isn't designed for this, but other folks seem to use it, and who am I to not be a sheep? I have 244 pathways and I get adjusted p-values for all but 29 of them. Howev ...
deseq2 written 11 days ago by ariel0
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Comment: C: Deseq2 post functional annotation for metagenome
... This is an active question in the community. Many papers use DESeq2. I am doing microbiome pathway analysis, and my KO and pathway abundances are mostly slightly bimodal, and certainly do not follow a negative binomial distribution (what the DESeq2 model is built around). In discussions, I've had a ...
written 6 weeks ago by ariel0
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Comment: C: DESeq2: handling NA values in colData
... If I understand correctly, you are saying I could do something like: ``` colData %>% mutate( somefactor = ifelse(is.na(somefactor), "MISSING", somefactor) %>% factor(levels=('ref', 'interesting', 'MISSING') ) ``` and then pull out the contrast `somefactor_interesting_vs ...
written 3 months ago by ariel0
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Comment: C: DESeq2 error due to zeros
... For the record, I 100% agree with you about 16s. However, it is being used in publications, and I'm an analyst, not the PI, so DESeq it is for the time being. ...
written 3 months ago by ariel0
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DESeq2 error due to zeros
... I'm getting the following error: > estimating size factors >Error in estimateSizeFactorsForMatrix(counts(object), locfunc = locfunc, : every gene contains at least one zero, cannot compute log geometric means However, I was under the impression that [DESeq2 could handle zeros][1] without pa ...
deseq2 written 3 months ago by ariel0 • updated 3 months ago by Michael Love26k
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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 9 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 9 months ago by ariel0 • updated 9 months ago by Michael Love26k
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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 9 months ago by ariel0

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