User: Ahill
Ahill • 1.5k
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Posts by Ahill
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Comment:
C: Subread alignment issue
... What operating system are you on? Did you install from a precompiled binary matched to your OS, or from from source? Have you tried posting to the support site or user group linked from the [subread home page][1]? Those contacts might be best source of help for a malloc error like this one.
[ ...
written 7 weeks ago by
Ahill • 1.5k
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C: Mean-variance trend in voom
... Rays on these types of plots extending from very low counts can sometimes be due to discretization of small integer counts (e.g, 0.5+0,1,2,3, ...) and variances particularly if n is small. How many replicates do you have included the mean/variance estimates? You could grab the source data from the ...
written 10 weeks ago by
Ahill • 1.5k
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... Interesting... I see the source of the Uniprot entry seems to be automated translation of the cDNA you linked from [this 1993 pub][1] (see figure 1). Paper suggests chain encoded by "HK102", a vK1 chain gene (as it was named in 1993?). There are many high-homology hits to this cDNA sequence in the ...
written 10 weeks ago by
Ahill • 1.5k
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... I see this issue has been raised on bioconductor (e.g. [here][1]). Not a statistician and interested to hear other views, but I'd say the DE methods in DESeq2 are valid for unbalanced groups; but they may be less optimal than if you had a balanced design with the same total sample size. You have a ...
written 11 weeks ago by
Ahill • 1.5k
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... If you are looking for precomputed gene or protein level interactions from text mining, have you seen [iHOP][1]? I've not looked at in quite a while but they did curate from PubMed "28.4 million sentences and 110,000 genes from over 2,700 organisms".
[1]: https://en.wikipedia.org/wiki/Informati ...
written 11 weeks ago by
Ahill • 1.5k
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... You mentioned "two types of treatments". If there is a third factor "treatment" in addition to time and batch that is not shown in the design matrix above can you add it? Colleagues have have had some good experience with `RUVg` in general but I'm not clear that your design matches their experienc ...
written 12 weeks ago by
Ahill • 1.5k
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... Ah, OK. If 'biological.phenomenom' is a binary label on each cell line (not an experimental factor that you modulated) then I suppose very confounded with cell.line effects. If cell.line effects are large (probably) but there are still 'biological.phenomenom' main effects that are large enough to ...
written 3 months ago by
Ahill • 1.5k
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... You describe that you are interested in finding genes most associated with the binary classification (versus building a predictor of your binary class?). If this is a gene selection question, I would think one alternative would be a differential expression approach: i.e. limma or equivalent with yo ...
written 3 months ago by
Ahill • 1.5k
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... What about comparing the Louvain modularity scores across your different k values? In principle, Dunn index can be applied to assess clustering results for any method that groups items, presuming you can compute distances between the items. Calculating the Dunn index on your clusters would tell yo ...
written 3 months ago by
Ahill • 1.5k
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... Yes, given the types you describe. RMA is on the log-2 scale. You've correctly calculated the fold change. 832 is a very big fold change, so might be very surprising but perhaps not impossible, depending on what your gene is and what the experimental conditions are. I'd agree that it is risky to ...
written 3 months ago by
Ahill • 1.5k
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For convert MACH .mlprob to Oxford .gen format
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For C: So what counts as a "novel" classifier?
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