Moderator: Mikael Huss

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Mikael Huss4.5k
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Posts by Mikael Huss

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Comment: C: pareto scaling of RMA normalised values for Principle component analysis (PCA)
... Center by using e g centered <- scale(matrix, center=TRUE, scale=FALSE) (or centered <- apply(matrix, 2, function(x) x - mean(x)) as in the code snipped I linked) Then Pareto scale using the above pareto.matrix <- apply(centered, 2, function(x) x/sqrt(sd(x))) ...
written 13 months ago by Mikael Huss4.5k
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Comment: C: pareto scaling of RMA normalised values for Principle component analysis (PCA)
... How can I do that when I don't know what your matrix looks like? It should be something like pareto.matrix <- apply(matrix, 2, function(x) x/sqrt(sd(x))) ...
written 13 months ago by Mikael Huss4.5k
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Answer: A: pareto scaling of RMA normalised values for Principle component analysis (PCA)
... Pareto scaling comes down to scaling each column (dividing each value in the column) by the square root of the standard deviation of the column's values. You could adapt the code from here as appropriate: https://github.com/cran/RFmarkerDetector/blob/master/R/scaling.R ...
written 13 months ago by Mikael Huss4.5k
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Answer: A: how to return the componenets from PCA back to original variables?
... I think you are looking for the loadings. Depending on which method you used in R, these could be in the "loadings" or "rotation" slot in the object returned from the PCA routine. The loadings tell you how the original variables are weighted to form each principal component. ...
written 13 months ago by Mikael Huss4.5k
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Comment: C: How to retrieve protein sequences in Diamond?
... One also needs to specify SAM output when viewing the output file, e g in your example diamond view -a matches -f sam ...
written 20 months ago by Mikael Huss4.5k
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Comment: C: How to retrieve protein sequences in Diamond?
... Yes, you need to specify the SAM output format. Good luck! ...
written 20 months ago by Mikael Huss4.5k
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Answer: A: How to retrieve protein sequences in Diamond?
... If you choose to view the output in SAM format, the sequence will be included as one of the output fields. It depends a bit on Diamond version where SAM output is specified - either as part of "diamond blastx" or "diamond view" (after the blastx step). Regarding the protein database, it's not clea ...
written 20 months ago by Mikael Huss4.5k
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Answer: A: How to tell viruses/bacteria found in human brain Rna-seq samples are intrinsic
... One possibility is that you are mapping to some type of vector. These are sometimes derived from viruses. You could try to filter against Univec or some other vector database. You could (although it is dull) try to go through some of these alignments and see if they are all stacking up to a certain ...
written 20 months ago by Mikael Huss4.5k
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Answer: A: Variant caller for low frequency variants
... You could try [LoFreq][1] (depending on exactly what your needs are). It's worked well for me with viruses, for example. [1]: http://csb5.github.io/lofreq/ ...
written 20 months ago by Mikael Huss4.5k
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Answer: A: Accessing Expression Levels for Genes of Interest from GEO Experiments
... The [EMBL-EBI Baseline Expression Atlas][1] offers a convenient interface for looking gene by gene (put your gene name in the search bar where it says "Enter gene query"). It summarized information from studies such as the already mentioned BodyMap and others. There is a column for smooth muscle (sc ...
written 20 months ago by Mikael Huss4.5k

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