User: Pekka Kohonen

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Pekka Kohonen190
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Sweden
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Posts by Pekka Kohonen

<prev • 32 results • page 1 of 4 • next >
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Comment: C: Getting data/objects to workers in bplapply inside a function
... Thanks! It worked beautifully! A very clever example code. ...
written 6 weeks ago by Pekka Kohonen190
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Getting data/objects to workers in bplapply inside a function
... I know that this question has probably been answered implicitly somewhere but I have read many answers online and it always seems to have been written in a way that I don't understand. The situation is that I have a function which uses bplapply and I want to pass data from the function call to bpla ...
biocparallel written 6 weeks ago by Pekka Kohonen190 • updated 6 weeks ago by Martin Morgan ♦♦ 20k
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Comment: C: BiocParallel on Windows : cannot find my functions when using SnowParam
... I have been trying to understand and read several posts about sending data (objects, functions, whatever) to workers. And I just can't seem to get it. It seems to be that the way that it is explained always is just impenetrable .... I have read about environments etc. I have a situation where I have ...
written 6 weeks ago by Pekka Kohonen190
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Comment: C: Extending limma to cover "non-linear" dose response models e.g. Hill, Exponenti
... Thanks for your answer!  ...
written 6 weeks ago by Pekka Kohonen190
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Comment: C: Extending limma to cover "non-linear" dose response models e.g. Hill, Exponenti
... Formulae for these models: Polynomial model: μ(dose)=β_0+β_(1 ) dose+ β_(2 ) 〖dose〗^2+ ⋯ + β_(n ) 〖dose〗^n where n is the degree of the polynomial. Linear model: The linear model is a special case of the polynomial model with n fixed at 1. Power model: μ(dose)=γ+ β_ 〖dose〗^δ where ...
written 6 weeks ago by Pekka Kohonen190
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Comment: C: Extending limma to cover "non-linear" dose response models e.g. Hill, Exponenti
... This is a bit complicated question. Maybe even a whole new research field :-). Just wanted to put it out there since I don't personally have the expertise to do the modifications to limma (I think). Doing gene expression data over multiple doses gives a whole new perspective on mechanisms of compoun ...
written 6 weeks ago by Pekka Kohonen190
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Extending limma to cover "non-linear" dose response models e.g. Hill, Exponential, etc...
... Hi, I wonder if analyses of "non-linear"-like dose-response data is or could be covered by limma. By dose response gene expression data I mean data with 5-10 doses (3-5 biological replicates) of a chemical treatment per time-point. Novel technologies, conceptually related to the LINCS project, e.g. ...
limma dose-response lincs tempo-seq high-throughput transcriptomics written 6 weeks ago by Pekka Kohonen190 • updated 6 weeks ago by Gordon Smyth32k
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Comment: C: Meta-Analysis after running limma on a normalized dataset
... I am not sure if it makes sense to do traditional meta-analysis on gene expression data. What I have found is that using packages such as RankProd works pretty well. You would take the directional t-statistics from limma, make a table out of them and then do one-sample RankProd analysis (or Ranksum ...
written 9 months ago by Pekka Kohonen190
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Comment: C: Statistic for GSA
... Hi, as far as I can tell they all use the moderated t-statistic in one way or another (i.e. roast, romer, camera, fry). It is also consistent with the limma philosophy to do so (Ritchie et al. 2015), as they stress the importance of the eBayes information borrowing and the variance trend modelling a ...
written 9 months ago by Pekka Kohonen190
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Comment: C: Statistic for GSA
... Thanks! I will probably use it for ssGSEA analysis at least! Is it able to do mixed or absolute gene set statistic analyses? There are some recent papers (Nam D. et al. 2015 and Yoon S. et al. 2016) which show (as far as I can tell) that use of the absolute statistic reduced the inter-gene correlati ...
written 9 months ago by Pekka Kohonen190

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