Moderator: Jean-Karim Heriche
Jean-Karim Heriche ♦ 15k
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- EMBL Heidelberg, Germany
- Website:
- http://jkh1.github.io/
- Last seen:
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- Joined:
- 6 years, 10 months ago
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Posts by Jean-Karim Heriche
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... For the tensor factorization, you start from the same 3d array you constructed following my indications above but you need to turn it into a tensor object before using it with the rTensor package, i.e.:
Ary <- as.tensor(Ary)
Not doing this is probably what causes the error. You must also re ...
written 14 hours ago by
Jean-Karim Heriche ♦ 15k
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... You can think of dtw as sequence alignment for multivariate data. Instead of aligning sequences of characters, it aligns sequences of multidimensional points. Just like sequence alignment, it returns a score (a distance) telling you how similar the two time series are. So you can compute all pairwis ...
written 3 days ago by
Jean-Karim Heriche ♦ 15k
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... As far as I remember, hmmbuild can read alignments in several formats. Just check the docs. ...
written 3 days ago by
Jean-Karim Heriche ♦ 15k
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... To give a bit more details, to build a HMM for a set of proteins, the steps are:
- build a multiple sequence alignment with e.g. Clustal
- run hmmbuild (from the HMMER package) with the multiple sequence alignment as input ...
written 6 days ago by
Jean-Karim Heriche ♦ 15k
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... Is dataframe1 really transposed compared to df2 and 3, i.e. patients in rows vs patients in columns ?
Anyway, for the dtw() function, you need the time points in rows and metabolites in columns for each patient so you need to transform your data with something like the untested code below (assumin ...
written 6 days ago by
Jean-Karim Heriche ♦ 15k
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... Yes. water uses the [DNAFULL matrix][1] by default for nucleotides, a custom one can be supplied with the option -datafile matrixf.
[1]: http://rosalind.info/glossary/dnafull/ ...
written 6 days ago by
Jean-Karim Heriche ♦ 15k
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... You should be able to do this with blastn setting the window size and other parameters appropriately or maybe with the option -task blastn-short. Otherwise, you can always use either the Needleman-Wunsch or the Smith-Waterman alignment algorithms. They are available as needle and water in the [EMBOS ...
written 7 days ago by
Jean-Karim Heriche ♦ 15k
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... I take it you don't know what a [z-score][1] is otherwise, could you please clarify why it should be between -1 and 1 ?
[1]: https://en.wikipedia.org/wiki/Standard_score ...
written 7 days ago by
Jean-Karim Heriche ♦ 15k
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... Two standard options:
- use dynamic time warping (see the [R package dtw][1]) and apply a clustering algorithm to the resulting distance matrix
- treat the data as a 3D tensor and apply a tensor factorization algorithm (see for example [my tutorial here][2])
[1]: http://dtw.r-forge.r-project ...
written 7 days ago by
Jean-Karim Heriche ♦ 15k
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Comment:
C: Functional enrichment of pathways
... Presented like this, this seems the wrong thing to do. If this is OK, then why not remove genes with annotations you don't like ?
I hope that at least this is mentioned when you report the results because on the face of it, this is fishing for significance.
Removing genes from a list has to be well ...
written 12 days ago by
Jean-Karim Heriche ♦ 15k
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