User: Gavin Kelly

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Gavin Kelly560
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560
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Location:
United Kingdom / London / Francis Crick Institute
Twitter:
gavinpaulkelly
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Last seen:
1 month, 2 weeks ago
Joined:
5 years ago
Email:
g*************@gmail.com

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

Posts by Gavin Kelly

<prev • 101 results • page 1 of 11 • next >
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Comment: C: How to compare the design formulas of DESeq2?
... 2 mice in each group is enough to allow you estimate interaction with some degrees of freedom left to assess statistical significance (well, you could even get away with 2 mice in just one of the groups, but I wouldn't recommend that!)  The question now becomes one of power to detect any changes, an ...
written 23 months ago by Gavin Kelly560
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Answer: A: should subgroups of comparisons be analyzed separately in Limma
... It is a judgement call, and your situation is one that many of us can sympathise with.  (1) is the 'correct' approach from a statistical point of view, if you've no reason to doubt that the variance in A and in B is roughly similar to the variance in C and  in D.  You get more power that way, and th ...
written 24 months ago by Gavin Kelly560
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Comment: C: Running DESeq2 with gene-dependent binary variable such as membership in pathway
... To me at least, it's unclear what could be achieved by this.  Membership of pathway is usually dealt with by something akin to GSEA after generating a statistic via DESeq2.  The only other thing I can of is subsetting your data by your binary variable, but there would be very little difference (if a ...
written 24 months ago by Gavin Kelly560
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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 2.0 years ago by Gavin Kelly560
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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 2.0 years ago by Gavin Kelly560
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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 2.0 years ago by Gavin Kelly560
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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 2.0 years ago by Gavin Kelly560
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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 2.0 years ago by Gavin Kelly560 • updated 2.0 years ago by Michael Love26k
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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 2.1 years ago by Gavin Kelly560
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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 2.1 years ago by Gavin Kelly560

Latest awards to Gavin Kelly

Good Answer 15 months ago, created an answer that was upvoted at least 5 times. For A: extracting the genes associated with the clusters
Scholar 2.4 years ago, created an answer that has been accepted. For A: About the results and contrast (DESeq2)
Scholar 2.4 years ago, created an answer that has been accepted. For A: Difference between DESeq2 1.14 and 1.16
Scholar 2.4 years ago, created an answer that has been accepted. For A: DESeq2 3-fatcor design and different interaction terms
Centurion 2.4 years ago, created 100 posts.
Appreciated 2.4 years ago, created a post with more than 5 votes. For A: extracting the genes associated with the clusters
Scholar 2.4 years ago, created an answer that has been accepted. For A: What's the criteria used by DESeq2 to calculate log2 fold changes in time-course
Scholar 2.4 years ago, created an answer that has been accepted. For A: ChIPseeker mapping between keys and columns
Scholar 2.4 years ago, created an answer that has been accepted. For A: deseq2 LRT vs Wald test results for DE expression among 4 conditions
Teacher 2.7 years ago, created an answer with at least 3 up-votes. For A: extracting the genes associated with the clusters
Scholar 2.7 years ago, created an answer that has been accepted. For A: DESeq2 3-fatcor design and different interaction terms
Autobiographer 2.7 years ago, has more than 80 characters in the information field of the user's profile.
Scholar 4.0 years ago, created an answer that has been accepted. For A: DESeq2 3-fatcor design and different interaction terms

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