User: Kevin Coombes

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Kevin Coombes430
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Posts by Kevin Coombes

<prev • 44 results • page 1 of 5 • next >
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Annotation DB for ArrayStar lncRNA arrays
... I'm helping someone analyze array data from the ArrayStar lncRNA 2.0 microarrays. The company claims that they can't or won't provide annotations for every probe on the array, since that information is proprietary. They will only provide it for probes that they found to be differentially expressed i ...
annotation annotationdbi arraystar lncrna written 4.4 years ago by Kevin Coombes430 • updated 4.0 years ago by xiangy70
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Comment: C: Looking for a function
... A long time ago, a company called InPharmix sold a tool called PDQ_Med that did exactly this. I don't think it ever caught on, but their web site from 2004 is still google-discoverable. They actually started from a list of genes (as in the results of a differential expression analysis) and disease ...
written 5.4 years ago by Kevin Coombes430
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Answer: A: Gene shaving for bioconductor?
... While it is not part of BioConductor, Bradley Broom ad Kim-Anh Do have implementations for R and for JavaScript (or in a browser) that is available at: http://bioinformatics.mdanderson.org/main/GeneClust:Overview On 12/18/2013 7:41 AM, January Weiner wrote: > Is there a package for gene shaving ...
written 5.7 years ago by Kevin Coombes430
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Comment: C: scholarly reference for "don't draw PCA/heatmap dendrograms on DEGs"
... I don't have a good reference either. But you can easily simulate matrices full of IID standard normal data, pick the "most differentially expressed" and show that this noise/nonsense perfectly separates any two "groups" that you want to pretend is present in the data. -- Kevin On 12/9/2013 8: ...
written 5.7 years ago by Kevin Coombes430
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Answer: A: [topGO] More flexible way to select 'interesting' genes
... That's because you (and many other people) actually want to filter on the (posterior) probability that the log fold change is bigger than some (prespecified) value that you believe is biologically meaningful. I have no idea how to accomplish this with topGO, but if you can find a way to compute that ...
written 6.0 years ago by Kevin Coombes430
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Comment: C: how to annotate Illumina HumanHT-12 v3 chips?
... My opinion: best = largest IQR (as a first approximation). Some probes are broken, and never give meaningful values; they tend to have small IQR. Keep in mind that this still does not deal with the fact that (regardless of what we or the companies designing the probes) might like to think, some pro ...
written 6.5 years ago by Kevin Coombes430
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Comment: C: Question about interpretation of CHARM results
... I understand all the statistical reasons for converting from methylation "beta values" to something logistic, and am frequently tempted to do this myself. But I think in the context of methylation that this advice should come with a warning: changes in levels near 0 and 1 may have a lot of leverage ...
written 7.0 years ago by Kevin Coombes430
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Answer: A: Normalization of array leads to decrease in number of differentially expressed g
... Normalizing separately is likely to lock in a bias that would be removed if you normalize together. So, I would be more inclined to believe the (fewer) differentially expressed genes that you find when normalizing together. On 7/25/2012 6:07 AM, Cytochalasin wrote: > Hi all, > > I perform ...
written 7.1 years ago by Kevin Coombes430
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Comment: C: expression status from pvalues
... It depends. In CLL, almost all of the copy number changes are single copy gains or single copy losses (for different genes). So the copy number data only has two levels, in which case correlation doesn't tell you very much and a one-sided t-test is better. Kevin On 7/12/2012 12:18 AM, Alyaa ...
written 7.1 years ago by Kevin Coombes430
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Comment: C: Influence of expression correlation on false positive ratio
... Hi Wolfgang, It's not just technical artifacts. Everyone believes (probably correctly) that gene expression in biological samples is in fact correlated, a fact that is exploited all the time when people run algorithms to try to (re)construct networks or pathways based on coexpression. And while I ...
written 7.1 years ago by Kevin Coombes430

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Popular Question 4.4 years ago, created a question with more than 1,000 views. For Annotation DB for ArrayStar lncRNA arrays

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