User: Gavin Kelly

gravatar for Gavin Kelly
Gavin Kelly510
Reputation:
510
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Trusted
Location:
United Kingdom / London / Francis Crick Institute
Twitter:
gavinpaulkelly
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Last seen:
5 days, 11 hours ago
Joined:
3 years ago
Email:
g*************@gmail.com

Statistician in the Bioinformatics & Biostatistics group at the Francis Crick institute

Posts by Gavin Kelly

<prev • 98 results • page 1 of 10 • next >
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Comment: C: lfcShrink and factors with multiple levels
... For 1a and 1b, you've swapped numerator and denominator - "Cond DM vs DP" is output by DESeq in 1a, but 1b reports it's calculating "Cond DP vs DM".  Using 'contrast' you specify the numerator first and the denominator (ie what would be the baseline for the 'coef' approach) second, so the flips you' ...
written 8 days ago by Gavin Kelly510
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Answer: A: change plot title in DNAcopy multiple plot.type="s"
... If we examine the source code of plot.DNAcopy then it appears the 'main' argument is hard-wired in.  My only suggestion is to copy the source into your own function, and modify the behaviour to give you want you want - I don't know of a way to capture the make-up of a base plot in a way that it can ...
written 13 days ago by Gavin Kelly510
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Answer: A: Design model for DESeq2 analysis
... Thanks for the extra info. So, there's (at least) two stages to "DESeq2 has run" - the DESeq command gives you the potential to ask many questions via the results command (by selecting the relevant 'contrast' or 'name' argument), of which your code is defaulting to the comparison between sexes.  Yo ...
written 15 days ago by Gavin Kelly510
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Comment: C: Design model for DESeq2 analysis
... Without showing us exactly how you got from dds to res, it's not possible to give much advice.  But I suspect that you're not specifying a contrast, and therefore you're letting DESeq chose the default contrast, which is the final term in your design.  So the ~ sex + condition model is the one that ...
written 15 days ago by Gavin Kelly510
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DESeq2 'results' usability issue
... Debugging someone's code, I just noticed a slight usability issue with the results function, which has a '...' argument, so when results(dds, contrasts=c("group","A","B")) was called, the spelling mistake of the contrast argument wasn't picked up with a usual 'unused argument' warning, and it defaul ...
deseq2 written 19 days ago by Gavin Kelly510 • updated 19 days ago by Michael Love15k
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Comment: C: DESEq2 for mulitple tissues under 2 conditions
... I'm guess that e.g. WA1 is replicate one of WA.  To get your analysis started, you'll at least need to separate out that using eg tidyr::extract(coldata, c("Tissue","Replicate", "(..)([123])")  . Then you'll probably need to clarify what exactly you mean by "between all tissue types" - do you want a ...
written 21 days ago by Gavin Kelly510
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Answer: A: Loop for mass analyses and extraction of FCS data
... It would be easier to diagnose if you gave the exact error message, but as a guess, flowcore::Subset requires the first argument be a flow object (such as your xNtrans ) whereas you're feeding it xN which is a character. ...
written 27 days ago by Gavin Kelly510
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Answer: C: results(dds) error: couldn't find results. you should first run DESeq()
... You've forgotten to assign the outputs of DESeq to anything; dds <- DESeq(dds) should sort things out for you ...
written 28 days ago by Gavin Kelly510
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Answer: A: Is my design appropriate for contrast in DESeq2?
... The difference will be that, in the single-dataset approach, you're estimating the variance (biological variability) by pooling the estimates within each treatment group.  This will give you greater power, so is generally the recommended approach.  Splitting the data into pairs of treatments will ha ...
written 28 days ago by Gavin Kelly510
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Comment: C: SC3 gene clusters
... And if you do run 'tmp <- pheatmap(...)', then tmp$kmeans$cluster will give you the clusters (though you might want to set.seed(1) so that you always get the same results!)   ...
written 4 weeks ago by Gavin Kelly510

Latest awards to Gavin Kelly

Scholar 8 months ago, created an answer that has been accepted. For A: DESeq2 3-fatcor design and different interaction terms
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: extracting the genes associated with the clusters
Autobiographer 8 months ago, has more than 80 characters in the information field of the user's profile.
Scholar 2.0 years ago, created an answer that has been accepted. For A: DESeq2 3-fatcor design and different interaction terms

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