User: heikki.sarin

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Posts by heikki.sarin

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Comment: C: Dealing with (blood) contamination in RNA-seq data
... Yeah, that indeed sounds quite bizarre that WBC would express haemoglobin etc gas exchange related genes.  1) If after RUVseq we still have the same results and there isn't any single high-expression samples in these genes do you see it as plausible that then the results might be genuine? 2) Is it ...
written 22 months ago by heikki.sarin0
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Comment: C: Dealing with (blood) contamination in RNA-seq data
... Little follow-up on the topic. We have RNA-seq gene and exon-level data extracted from white blood cells. We have significant hits on various hemoglobin, haemoglobin metabolic processes and gas exchange related genes from the differential expression analysis. Foldchanges are quite small and vary bet ...
written 22 months ago by heikki.sarin0
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goseq: In pcls(G) : initial point very close to some inequality constraints
... Hi, I'm running pathway analysis with goseq but had the error : In pcls(G) : initial point very close to some inequality constraints : when plotting the nullp. I'm not sure if this is an issue or not. The curve doesn't start on the y-axin from zero but 0.004 but after that the curve is pretty simil ...
goseq mgcv pwf warning message written 22 months ago by heikki.sarin0 • updated 22 months ago by Nadia Davidson280
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limma: The topTable function implementation when outputin the differential expression results from RNA-seq dataset?
... Hi, So I'm trying to test differential gene expression on case/control study across all time points when accounting for the within subject variability. I know the full and reduced models between which I want to test (if I could use LRT) with but I'm a bit unsure how to apply it to the limma+voom pi ...
limma edger toptable voom output written 22 months ago by heikki.sarin0 • updated 22 months ago by Aaron Lun24k
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Comment: C: edgeR: How to set model for glmQLFTest in time-course experiment (compared to gl
... Well, that's good to hear. Yeah, on average around 100 million reads and highest ones a bit over 200 million.  ...
written 22 months ago by heikki.sarin0
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Comment: C: edgeR: How to set model for glmQLFTest in time-course experiment (compared to gl
... Yeah, I've done pre filtering before the analysis in two steps: 1) remove.zeros=TRUE  (when creating the DGEList object) 2) A <- rowSums(dge$counts) dge <- dge[A>10, ,keep.lib.sizes=FALSE] Should I do more aggressive pre-filtering or is it possible that the plots are fine? Also on the Di ...
written 22 months ago by heikki.sarin0
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Comment: C: edgeR: How to set model for glmQLFTest in time-course experiment (compared to gl
... Thank you very much! Little follow-up on the matter. Is it an issue if on plotQLDisp() the Average Log2 CPM value axis and the values plotted start from -5 ? Otherwise the plot seems symmetrical and somewhat similar to the ones in the user guide.  ...
written 22 months ago by heikki.sarin0
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Comment: C: edgeR: How to set model for glmQLFTest in time-course experiment (compared to gl
... There is no problems or errors when running the glmQLFit and glmQLFTest instead of LRT approach. The point of interest on the matter is that is the statistical background of both approaches similar in such way that if I also set the coef=35:36  in glmQLFtest the test will produce an answer to the sa ...
written 22 months ago by heikki.sarin0
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edgeR: How to set model for glmQLFTest in time-course experiment (compared to glmLRT?
... Hi,  We have an experiment model:  ~ condition + time + condition:subject.nested + condition:time . We're trying find any differentially expressed genes/exons between condition groups across any of the timepoints when accounting for the within subject variability. When we setup the model.matric we ...
timecourse edger model edger "glmqlftest()" written 22 months ago by heikki.sarin0 • updated 22 months ago by Ryan C. Thompson7.3k
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Comment: C: edgeR : How to test differential exon expression on case/control study across al
... 1)Thank you for making that clear. The concept of LRT is very familiar to me but the main problem was to understand how does glmLRT function and the coef argument have to be set so that I get what I'm trying achieve. As contrast, I've been using also DESeq2 for gene-level testing and there one can s ...
written 22 months ago by heikki.sarin0 • updated 22 months ago by Gordon Smyth37k

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