User: Stijn van Dongen
Stijn van Dongen • 80
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- 4 years, 8 months ago
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- 9 years, 11 months ago
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Posts by Stijn van Dongen
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... 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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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 ...
written 4.7 years ago by
Stijn van Dongen • 80
• updated
4.7 years ago by
Steve Lianoglou ♦ 12k
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...
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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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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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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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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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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