User: Stijn van Dongen

gravatar for Stijn van Dongen
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Posts by Stijn van Dongen

<prev • 10 results • page 1 of 1 • next >
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Comment: C: voom/limma contrast for comparing one level against base-line
... Thanks very much for the feedback. I tested Ryan's code, and it gives the same result as my original code. The code by Aaron seems to give different results.  As Aaron's description "compare cell line B with the average expression of all other cell lines" is in fact what I aim for, I now wonder what ...
written 4.7 years ago by Stijn van Dongen • 80
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voom/limma contrast for comparing one level against base-line
...   Hello, I am not completely sure I am doing the analysis correctly (see below).  I have RNA seq data for 20 cell lines for the same tissue, each cell line in triplicate. The pdata file thus basically looks like this: celltype A1 A A2 A A3 A B1 B B2 B B3 B .... I would like to contrast the ...
limma voom contrast written 4.7 years ago by Stijn van Dongen • 80 • updated 4.7 years ago by Steve Lianoglou ♦ 12k
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Answer: A: Trimming of partial adaptor sequences
... This is an answer I sent off-list to Sean, but I am sending to the list as some other responses may indicate this is topical: We recently published 'Kraken', a suite of tools for NGS processing (the umpteenth, indeed). It has extensive facities for adapter trimming though, as we do a lot of small ...
written 6.4 years ago by Stijn van Dongen • 80
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Comment: C: cluster genes based on expression pattern
... On Fri, Jun 17, 2011 at 10:49:08AM +1000, Moshe Olshansky wrote: > Hi Rabe, > > You can check timecourse package (Bioconductor). > Sean's suggestion to filter genes is always a good idea. > My naive approach would be to define a sensible distance between two genes > and use this d ...
written 8.5 years ago by Stijn van Dongen • 80
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Comment: C: booklet on using R for biomedical statistics
... For what it's worth, I found it quite interesting. On Mon, Dec 13, 2010 at 03:36:52PM -0000, Coghlan, Avril wrote: > Dear Vincent, > > Sorry about that.. I had thought it could be of interest to people on this list. > > Regards, > Avril > > -----Original Message----- > F ...
written 9.0 years ago by Stijn van Dongen • 80
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Comment: C: Group millions of the same DNA sequences?
... On Thu, Nov 18, 2010 at 09:21:07AM +0800, Xiaohui Wu wrote: > Thank you Aaron! Till now, sort and uniq may be the easiest way to do this. > For clustering, I don't think assembler is suitable for my case. I want to > cluster similar reads to get different clusters, each cluster has some r ...
written 9.1 years ago by Stijn van Dongen • 80
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Comment: C: Fastest way to read CSV files
... sorry, this: > <----integer 1 ---> <--- integer 2 ---> > 0000000 0014 0000 4268 0000 0000 0000 c000 4070 should have been: <-int 1-> <-int 2-> 0000000 0014 0000 4268 0000 0000 0000 c000 4070 > Thanks Misha, that's very instructive. > I'd like ...
written 9.3 years ago by Stijn van Dongen • 80
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Comment: C: Fastest way to read CSV files
... Thanks Misha, that's very instructive. I'd like to add that this can be made quite parametrizable, in that it is possible to write and read the dimensions of the object as well. In fact, by writing some kind of 'cookie' number it would be possible to have code that can recognize what *type* of data ...
written 9.3 years ago by Stijn van Dongen • 80
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Comment: C: Fastest way to read CSV files
... This piqued my interest, as for really large datasets it can in general speed up things greatly to use binary formats (1.5 million does not sound *that* big to me). I have no experience with this in R, but a little search brought up e.g. readBin(). So it might be possible, especially if your data i ...
written 9.3 years ago by Stijn van Dongen • 80
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Answer: A: identifying network communities in a protein-protein interaction graph
... Hi All, hi Avril, On Mon, Jan 18, 2010 at 05:10:53PM -0000, Coghlan, Avril wrote: > Dear all, > I am wondering is there any function available in Bioconductor or other > R libraries for detecting network communities in protein-protein > interaction graphs (where a "network commun ...
written 9.9 years ago by Stijn van Dongen • 80

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