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Martin Morgan | 1 Dec 2011 01:25

Bioconductor Employment: Statistical Research Associate

Bioconductors! -- please see the job description below for a Statistical 
Research Associate opening with the Bioconductor group. See

   http://fhcrc.org/about/jobs/index.html

choose 'Search Jobs' at the Fred Hutchinson Cancer Research Center, and 
look for job ID 24198 for a complete job description. Please contact me 
directly with any questions.

Best,

Martin

----

The Bioconductor project (http://bioconductor.org) seeks a creative and 
motivated individual to join our bioinformatics team. Bioconductor 
develops and distributes open-source, open-development software for 
analysis and comprehension of high-throughput genomic data from 
sequencing and other sources. Bioconductor is based on the R language 
for statistical analysis, with more than 500 software packages developed 
internally and by our vibrant user community.

SCOPE OF RESPONSIBILITIES:

This unique opportunity links scientific research with software 
development. The applicant will work under immediate technical direction 
to analyze and comprehend high-throughput sequence data, translating 
their research insights into appropriate Bioconductor work flows.
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Dana.Stanley | 1 Dec 2011 02:18
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how to add a table to AnnotationDbi sqlite database?

Hi all

I am trying to use goProfyles with my custom chicken database GGal.db. The package is looking for the file in
my database that does not exist :

Error in eval(expr, envir, enclos) : object 'GGal.dbENTREZID' not found

I can make a simple table linking my ID and entrez id that the package is looking for, but I could not figure out
how to add it to the database...
To all of you reading posts and helping others a big THANKS.

Dana

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MacDonald, James | 1 Dec 2011 03:14
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Re: Probe level normalization

Hi Suresh,

Hypothetically you could do something like

dat <- ReadAffy()
dat <- bg.correct(dat, "rma")
dat <- normalize(dat, method = "quantiles")

Which will give you the normalized, background corrected probes. I doubt 
limma will take an AffyBatch as input, so you would have to extract the 
probes using the exprs() extractor.

Alternatively, you could use the affyPLM package, which stands for affy 
Probe Level Model. You can specify different probe level models - see 
the vignette for more information.

Best,

Jim

On 11/30/11 6:19 PM, suri ghani wrote:
> Hi,
>
> I am using affymetrix platform for expression analysis.
> I need to perform  the normalization of each of  individual probes 
> intensities which belong to a probeset (without the summarization of 
> individual probe intensities of a probeset). Further I would like to 
> perform statistical analysis on the normalized intensities of the 
> individual probes to identify those probes that are significantly 
> regulated between different conditions or treatments.
(Continue reading)

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Gordon K Smyth | 1 Dec 2011 04:06
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Limma Dual Color Agilent : Mixed model or not?

Dear Guillaume,

Not all questions have brief answers!  However see the short paper

   http://www.statsci.org/smyth/pubs/ISI2005-116.pdf

which is referenced on the help page for lmscFit.  The paragraph on page 2 
starting "Replicated arrays" explains why I would recommend a standard 
log-ratio analysis for the model you have fitted.

In general, the separate channel analysis gives more DE genes than a 
standard log-ratio analysis because it makes more model assumptions (of 
common intra-spot correlation) and recovers information from the A-values 
which is otherwise ignored.  An additional reason in your case is that you 
are imputing data for the separate channel analysis, so there are more non 
NA data values being used than for the log-ratio analysis.  For the model 
you have fitted, there is actually no information in the A-values to 
recover, so I would not do it.

Your targets frame seems to include other variables (RepNum and Polarity) 
not used in the analysis, but I assume you have good reasons to ignore 
them.

Best wishes
Gordon

> Date: Tue, 29 Nov 2011 16:10:02 +0100
> From: Guillaume Meurice <guillaume.meurice@...>
> To: Bioconductor mailing list <bioconductor@...>
> Subject: [BioC] Limma Dual Color Agilent : Mixed model or not ?
(Continue reading)

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Chintan Vora - Xcelris | 1 Dec 2011 08:03

cummeRbund Error in Volcano Plot

Hi,

I am trying to plot different graphs using cummerRbund for bacterial 
transcriptome.
I get all the plots except the volcano plot.

I am using : tophat-1.3.3.Linux_x86_64, samtools-0.1.12a, 
cufflinks-1.2.0.Linux_x86_64

I get following error:

library("cummeRbund")
cuff = readCufflinks()
cuff
gene = genes(cuff)
v = csVolcano(gene)
v
Error in grid.pretty(range) :
   infinite axis extents [GEPretty(-1.79769e+308,1.79769e+308,5)]

Can someone please explain where am i going wrong?

R session info is given below:

sessionInfo()
R version 2.14.0 (2011-10-31)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
(Continue reading)

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Joern Toedling | 1 Dec 2011 11:06
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Re: Fwd: Re: Installing Bioconductor packages on R 2.14.0 *without* administrator rights / from a script

Hello,

without touching upon any recent changes in biocLite, I would recommend 
the following simple way to install packages without administrator rights.

1. Create an environment variable called "R_LIBS" and point that a 
writeable directory where you want your packages to go to. For example 
in the ~/.bashrc set something like:
export R_LIBS="${HOME}/rpackages"
Syntax is bit different for other shells and I guess it's possible to do 
this under Windows as well.
2. Start up R and install packages using biocLite() or 
install.packages(). The directory defined in the variable "R_LIBS" will 
be the first entry returned by ".libPaths()"  (verify that) and thus 
used as default installation directory.

HTH,
Joern

On 11/29/2011 10:02 AM, andrea.grilli@... wrote:
> Hi Firas,
> I had similar problems working in linux. If it's also your case, I 
> solved changing administrative privileges to paths were all packages 
> are installed:
> sudo chmod 777 -R /usr/lib/R
> sudo chmod 777 -R /usr/local/lib/R/site-library
>
> Maybe this is not the conventional way, but allows me to update all 
> libraries without creating a new personal folder each time R is 
> updated to a new version.
(Continue reading)

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Alnaji, Fadi | 1 Dec 2011 11:51
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ddCt isn't working with exported ABI7500-RT-PACR file

Hello 

I am trying to use the ddCt package which was developed by Jitao David
Zhang, Rudolf Biczok and Markus Ruschhaupt. My problem is that it seems
the package is not able to read the exported file, the one contains the
individual ct Values, from ABI 7500 RT-PCR instrument. When I execute
the package, it says your file is not .SDM. That's true, as my file is
SDS, but this is the only possibility I have got in the machine. However
I tried to play a bit with the text format in excel to make SDS as
similar as the SDM in the package-example file. It worked indeed, but it
is not a practical way I believe. 

Is there any other option to make this package able to read my SDS
files, or to convert this file to SDM. 

Many thanks.  

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James Perkins | 1 Dec 2011 12:42
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Re: ddCt isn't working with exported ABI7500-RT-PACR file

Hey,

You could try ReadqPCR or HTqPCR, both enable you to read in SDS files
I believe (ReadqPCR has a read.qPCR function, and there is an
explanation of how to do so in HTqPCR). If you were to have problems
using your version of SDS file with ReadqPCR, I would be very grateful
if you could email me your file (annonymsed if you wish of course) so
I can alter ReadqPCR appropriately.

Cheers,

Jim

On 1 December 2011 10:51, Alnaji, Fadi <F.Alnaji@...> wrote:
>
> Hello
>
> I am trying to use the ddCt package which was developed by Jitao David
> Zhang, Rudolf Biczok and Markus Ruschhaupt. My problem is that it seems
> the package is not able to read the exported file, the one contains the
> individual ct Values, from ABI 7500 RT-PCR instrument. When I execute
> the package, it says your file is not .SDM. That's true, as my file is
> SDS, but this is the only possibility I have got in the machine. However
> I tried to play a bit with the text format in excel to make SDS as
> similar as the SDM in the package-example file. It worked indeed, but it
> is not a practical way I believe.
>
> Is there any other option to make this package able to read my SDS
> files, or to convert this file to SDM.
>
(Continue reading)

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Alnaji, Fadi | 1 Dec 2011 13:22
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Re: ddCt isn't working with exported ABI7500-RT-PACR file

Deam Jim, thanks a lot. 

I'll try this out and let you know. 

All the best - Fadi 

-----Original Message-----
From: jimrperkins@...
[mailto:jimrperkins@...] On Behalf Of James Perkins
Sent: 01 December 2011 11:42
To: Alnaji, Fadi
Cc: bioconductor@...
Subject: Re: [BioC] ddCt isn't working with exported ABI7500-RT-PACR file

Hey,

You could try ReadqPCR or HTqPCR, both enable you to read in SDS files
I believe (ReadqPCR has a read.qPCR function, and there is an
explanation of how to do so in HTqPCR). If you were to have problems
using your version of SDS file with ReadqPCR, I would be very grateful
if you could email me your file (annonymsed if you wish of course) so
I can alter ReadqPCR appropriately.

Cheers,

Jim

On 1 December 2011 10:51, Alnaji, Fadi <F.Alnaji@...> wrote:
>
> Hello
(Continue reading)

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km | 1 Dec 2011 15:14
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Re: custom SNPlocs / BSgenome package

Hi,

On Mon, Nov 28, 2011 at 8:00 AM, Valerie Obenchain <vobencha@...>wrote:

> Hi kmo,
>
> For the BSgenome, you can follow the "How to forge a BSgenome data
> package" document,
>
>    http://bioconductor.org/**packages/2.10/bioc/html/**BSgenome.html<http://bioconductor.org/packages/2.10/bioc/html/BSgenome.html>
>
> I'm not sure what you mean by "a SNPlocs package for it". The SNPlocs
> packages are all Homo sapiens and created from each dbSNP build. They can
> be found here,
>
>    http://www.bioconductor.org/**packages/release/data/**annotation/<http://www.bioconductor.org/packages/release/data/annotation/>
>
> Are you asking about creating a snp annotation package for a different
> organism?
>
>
Yes how do I include  snp annotation package of a different organism ?
Thanks
kmo

>
>
>
> On 11/26/11 11:03, km wrote:
>
(Continue reading)

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