## User: ariel

ariel0
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#### Posts by ariel

<prev • 20 results • page 1 of 2 • next >
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... 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 6 weeks 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 6 weeks ago by ariel0
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... 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 ...
written 7 weeks ago by ariel0 • updated 7 weeks ago by Michael Love25k
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... 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 7 months ago by ariel0
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... 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 ...
written 7 months ago by ariel0 • updated 7 months ago by Michael Love25k
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... 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 7 months ago by ariel0
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... 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 7 months ago by ariel0
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... 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 7 months ago by ariel0
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... 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 7 months ago by ariel0
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... Right-O. Sorry I missed that. ...
written 7 months ago by ariel0

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