User: aquaq

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aquaq10
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1 year, 7 months ago
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Posts by aquaq

<prev • 17 results • page 1 of 2 • next >
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Rna-seq: How to normalize them with biological replicates to get change ratio?
... We have a cell line with certain plasmids added. The initial sample was split into three subsamples, plus it was sequenced once. The three subsamples were grown differently, then each sequenced once (of course the four library was pooled begore sequencing with their respective barcodes added). The s ...
rna-seq written 6 months ago by aquaq10
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Comment: C: Why do they use ratios for differential expression analysis?
... Thanks. I was thinking on microarray and realozed that with flurescency, it might be ratio scale. However, I've read that RNA-Seq measure counts relative to the number of all reads, and absolute quantification would be possible by adding controls (spikes). ...
written 6 months ago by aquaq10
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Why do they use ratios for differential expression analysis?
... I was interested in differential expression and started to read related materials. They all state that both RNA-seq and microarray data gives relative abundances (I understand that both can be absolute with some reference). As far as I know, this means interval scale instead of ratio scale. Then, th ...
differential expression statistics written 6 months ago by aquaq10
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Comment: C: What makes a good bionformatics prediction service?
... Thank you! I will make a mental not to myself - finding the right expression may worth a lot more than dozens of words. Just to enhance other's "forum experience". ...
written 9 months ago by aquaq10
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Comment: C: What makes a good bionformatics prediction service?
... My question is **not about the performance** of the predictions but rather how to make their usage user-friendly by setting up webpages that are easily usable, stable and provide all the features that would help the work of a user (both other bioinformaticians and experimentalist researchers). As ...
written 9 months ago by aquaq10
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Comment: C: What makes a good protein properties prediction service?
... I'm sorry, I have to revert it, I have already added 'bioinformatics'. Protein properties were only examples for a question above, I am interested in all kinds of bioinformatics prediction services in general. ...
written 9 months ago by aquaq10
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Comment: C: What makes a good prediction server?
... Thanks for the feedback, I will try to make myself clearer: bioinformatics researchers often make prediction services for protein structure/function/subcellular localizations/interactions/PTMs/glycolization/disorder/transmembrane topology whatever (same things apply for DNA/RNA predictions but I am ...
written 9 months ago by aquaq10
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Forum: What makes a good bionformatics prediction service from the point of user experience?
... Most of us tried to use one or more bioinformatics prediction services. We probably all have came across good and bad ones. How do you decide which one to use? What features make it more/less probable that you would stick to one? Let's assume that the underlying algorithms have the same performance. ...
server good forum prediction service written 9 months ago by aquaq10
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Comment: C: Calculate the coverage of a protein having a list of its peptides
... Just what I would do. I don't think, there is simpler solution. ...
written 10 months ago by aquaq10
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Answer: A: Elastic net (glmnet) predictive modeling: signal lost in noise
... You could use [care][1]t package to tune for glmnet parameters. Here is a nice example of the process: http://rstudio-pubs-static.s3.amazonaws.com/14372_1700240153ae4c2190feb1c5ced2d1e5.html [1]: http://topepo.github.io/caret/index.html ...
written 10 months ago by aquaq10

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