User: bdy8

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bdy80
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Posts by bdy8

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Comment: C: stringasfactor = F changes the output of pheatmap, why?
... Hi Wolfgang Looking a little bit deeper into what you suggested I think this is what is causing the problem. I am working on getting some reproducible code so people can run the code. Thank you for the response. Ben ...
written 9 weeks ago by bdy80
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Comment: C: stringasfactor = F changes the output of pheatmap, why?
... HI James First of all I apologise, i blanked on the self-contained code part and it now makes sense. I will try and make this work now (i.e. some reproducible code). Ben ...
written 9 weeks ago by bdy80
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Comment: C: stringasfactor = F changes the output of pheatmap, why?
... Hi James I am sorry if it was not clear, the code for the two heat-maps is exactly the same. As I shared above, the code for the heatmaps is again below, and it is ordered so it produces the first heatmap, then the second as in my original post. Note the only difference being the stringasfactors ar ...
written 9 weeks ago by bdy80 • updated 9 weeks ago by James W. MacDonald49k
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stringasfactor = F changes the output of pheatmap, why?
... Good Morning All I have a quick question that I cannot seem to work out why it is happening. As default, I have my R setup as stringasfactor = T. When using this i produce the following heat-map (second image) But, when I set stringasfactor=F, using the exact same input for the heat-map i get a ...
deseq2 pheatmap written 9 weeks ago by bdy80 • updated 9 weeks ago by Wolfgang Huber13k
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Comment: C: Quicker way to contrast multiple genotypes with treatment in DeSeq2
... thanks so much Michael. I just wanted to check to make sure I was not missing anything.  A loop it is.  ...
written 6 months ago by bdy80
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Quicker way to contrast multiple genotypes with treatment in DeSeq2
... Hi Bioconducter Land My query is similar to this other post (https://support.bioconductor.org/p/67600/#67612) which Michael Love provided a great answer to. I understand fully how to do this I was just wondering if there is a quicker/cleaner way to run through all my comparisons in DeSeq2.  Like t ...
deseq2 written 6 months ago by bdy80 • updated 6 months ago by Michael Love22k
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Comment: C: WGCNA extract genes from a module
... Hi Peter Thank you so much. I was not able to find your new site for the life of me.  It is all working now. Have a great Friday and weekend.  ...
written 7 months ago by bdy80
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WGCNA extract genes from a module
... Hi there everyone I am only posting this question as every other response to this topic suggest to use an example from a website which, using many different sources, I get a 404 error or site not found. This common answer site is posted below http://www.genetics.ucla.edu/labs/horvath/CoexpressionN ...
wgcna wgcna package written 8 months ago by bdy80 • updated 8 months ago by Peter Langfelder1.8k
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Comment: C: Group Specific Condition Query
... Hi Michael  Thank you so much for the help. It has answered where I was confused with the nesting within groups section.  The main problem I think I have had is applying this into DeSeq. With your clarification I understand exactly what I need to do with the analyses. I will be having my models an ...
written 8 months ago by bdy80
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Comment: C: Group Specific Condition Query
... Hi Michael Yes, year is a nuisance variable at this point. I have been doing some extra reading and think that a model with ~ Year + Genotype + Treatment (year being the nuisance/batch here) would be a much simpler model to use. This would, if I am correct in my thinking, allow analysis of the diff ...
written 8 months ago by bdy80

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