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>Today's Topics:
>
>   1. Open-rank faculty position, Dept of Biostatistics, Virginia
>      Commonwealth University (Kellie J Archer/FS/VCU)
>   2. Re: question on easyRNASeq developer version (Yanju Zhang)
>   3. Re: question on easyRNASeq developer version (Nicolas Delhomme)
>   4. Re: question on easyRNASeq developer version (Yanju Zhang)
>   5. Re: Error of GTF Annotation in easyRNASeq (Nicolas Delhomme)
>   6. Feature request in readVcf (Sean Davis)
>   7. Re: Feature request in readVcf (Tim Triche, Jr.)
>   8. Re: GO annotation (Marc Carlson)
>   9. Re: GO annotation (Srinivasan, Sathish  K)
>  10. Is normalization in edgeR required for small RNA sequencing
>      data? (Daniela Lopes Paim Pinto)
>  11. NGS public data analysis (Jill Pleasance)
>  12. Re: GO annotation (KJ Lim)
>  13. Analysis of public GEO datasets - NGS (Jill [guest])
>  14. Re: Is normalization in edgeR required for small RNA
>      sequencing data? (Mark Robinson)
>  15. Euro Bioc Devel 2012 Zurich CH -- Dec 13-14 2012 --
>      registration open (Mark Robinson)
>
>
>----------------------------------------------------------------------
>
>Message: 1
>Date: Fri, 21 Sep 2012 09:45:27 -0400
>From: Kellie J Archer/FS/VCU <kjarcher@vcu.edu>
>To: bioconductor@r-project.org
>Subject: [BioC] Open-rank faculty position, Dept of Biostatistics,
>        Virginia Commonwealth University
>Message-ID:
>    <OF6C640745.B02ABA54-ON85257A80.004B92B2-85257A80.004B92C1@vcu.edu>
>Content-Type: text/plain; charset="ISO-8859-1"
>
>
>The Department of Biostatistics at Virginia Commonwealth University
>(VCU) is
>seeking to fill a tenured/tenure-eligible faculty position at the level
>of
>assistant, associate, or full professor. We are seeking applicants with
>training and research interest in the design and statistical analysis
>of
>high-throughput genomic data (e.g., next generation sequencing,
>microarray,
>proteomic technologies), bioinformatics, computational biology, or
>closely
>related area. Additionally, applicants should have collaborative
>research
>experience.  Primary responsibilities include teaching and advising
>graduate
> students as well as conducting independent methodological research. In
>addition, the successful applicant will be expected to collaborate with
>other VCU investigators in related fields in obtaining extramural grant
>   support.
>
>The Department of Biostatistics has a 40+ year history in the VCU
>School of
>Medicine and is committed to excellence in both biostatistical research
>and
>graduate education. The department offers both M.S. and Ph.D. programs
>in
>Biostatistics, including a  concentration in Genomic Biostatistics, a
>M.S.
>in Clinical Research in Biostatistics, and a Master of Public Health.
>Our
> biostatistics  faculty,  students, and staff collaborate with clinical
>investigators on the Medical College of Virginia Campus (which includes
>the
>Schools of Medicine, Dentistry, Pharmacy, Nursing, and Allied Health)
>in a
>wide variety of biomedical research projects. Located in Richmond,
>Virginia,
>VCU has established relationships with the Virginia Department of
>Health as
>   well as local and regional health departments.
>
> Qualifications:  For  all  levels,  candidates  should have a Ph.D. in
>biostatistics, statistics or related field, demonstrated experience in
>the
>analyses of high-throughput genomic or proteomic data, familiarity with
>statistical programming environments for analyzing such data, and
>excellent
>   oral and written communication skills.
>
>   By Level of Appointment:
>
> Full  Professor:   Applicants  should have an established track record
> publishing  in  peer-reviewed journals, have national or international
>prominence in their area of expertise, and have demonstrated experience
>   obtaining extramural research support.
>
>Associate Professor: Applicants should have an established track record
>  publishing in peer-reviewed journals and have demonstrated experience
>      obtaining extramural research support.
>
>      Assistant Professor: Applicants should have at least two years of
>experience beyond completion of their degree program and must
>demonstrate
>      excellent oral and written communication skills.
>
>All candidates should have demonstrated experience working in and
>fostering
>a diverse faculty, staff, and student environment or commitment to do
>so as
>a faculty member at VCU.   Potential candidates can submit
>applications,
>including a statement of research, teaching philosophy, curriculum
>vitae and
>contact information for three professional references, via mail ??? to
>Yvonne
>Hargrove, Department of Biostatistics, Virginia Commonwealth
>University,
>P.O.   Box   980032,  Richmond,  VA  23298-0032  ???  or  by  e-mail
>to
>   yfhargro@vcu.edu.
>
>Virginia Commonwealth University is an equal opportunity/affirmative
>action
>employer.  Women, minorities and persons with disabilities are
>encouraged to
>   apply.
>   Kellie J. Archer, Ph.D.
>   Associate Professor, Department of Biostatistics
>   Director, VCU Massey Cancer Center Biostatistics Shared Resource
>   Virginia Commonwealth University
>   830 East Main St., 718
>   Richmond, VA 23298-0032
>   phone: (804) 827-2039
>   fax: (804) 828-8900
>   e-mail: kjarcher@vcu.edu
>   website: www.people.vcu.edu/~kjarcher
>
>
>------------------------------
>
>Message: 2
>Date: Fri, 21 Sep 2012 16:32:58 +0200
>From: Yanju Zhang <hollandorange.yanju@gmail.com>
>To: Nicolas Delhomme <delhomme@embl.de>
>Cc: bioconductor@r-project.org
>Subject: Re: [BioC] question on easyRNASeq developer version
>Message-ID:
>   <CABNzwf6NfM0eqs_Ht3N5McQcN=mBfKt+GUtYCObsm2gWYaYCow@mail.gmail.com>
>Content-Type: text/plain
>
>Hi Nico
>As mentioned in SEQAnswers, I also encountered this problem:
>
>> "Error in mk_singleBracketReplacementValue(x, value) :
>> 'value' must be a CompressedIntegerList object"
>
>In my bam files, the reads are with different length.
>
>I am expecting the solution. If you need more information, please let
>me know.
>
>Best wishes
>Yanju
>
>        [[alternative HTML version deleted]]
>
>
>
>------------------------------
>
>Message: 3
>Date: Fri, 21 Sep 2012 16:37:13 +0200
>From: Nicolas Delhomme <delhomme@embl.de>
>To: Yanju Zhang <hollandorange.yanju@gmail.com>
>Cc: bioconductor@r-project.org
>Subject: Re: [BioC] question on easyRNASeq developer version
>Message-ID: <AAFB721C-86AF-49BF-ACF8-47AE5DBA320D@embl.de>
>Content-Type: text/plain; charset=us-ascii
>
>Hi Yanju,
>
>Would you be OK with uploading the file that creates the problem on my
>dropbox? If that's OK, I'll send you a link to it. That would be best
>for me to reproduce the error.
>
>Cheers,
>
>Nico
>
>---------------------------------------------------------------
>Nicolas Delhomme
>
>Genome Biology Computational Support
>
>European Molecular Biology Laboratory
>
>Tel: +49 6221 387 8310
>Email: nicolas.delhomme@embl.de
>Meyerhofstrasse 1 - Postfach 10.2209
>69102 Heidelberg, Germany
>---------------------------------------------------------------
>
>
>
>
>
>On Sep 21, 2012, at 4:32 PM, Yanju Zhang wrote:
>
>> Hi Nico
>> As mentioned in SEQAnswers, I also encountered this problem:
>> > "Error in mk_singleBracketReplacementValue(x, value) :
>> > 'value' must be a CompressedIntegerList object"
>>
>> In my bam files, the reads are with different length.
>>
>> I am expecting the solution. If you need more information, please let
>me know.
>>
>>
>> Best wishes
>> Yanju
>>
>>
>
>
>
>------------------------------
>
>Message: 4
>Date: Fri, 21 Sep 2012 17:54:21 +0200
>From: Yanju Zhang <hollandorange.yanju@gmail.com>
>To: Nicolas Delhomme <delhomme@embl.de>
>Cc: bioconductor@r-project.org
>Subject: Re: [BioC] question on easyRNASeq developer version
>Message-ID:
>   <CABNzwf45nimkWg3guqJWBYqQqhxBW7qMPd4dX_S9WXJh13vO2w@mail.gmail.com>
>Content-Type: text/plain
>
>Hi Nico,
>
>It is fine with me to upload my bam file. Please give me the link.
>
>Best wishes
>Yanju
>
>Code + error + sessionInfo
>> chr.sizes=as.list(seqlengths(Hsapiens))
>> bamfiles=dir(getwd(),pattern="*.sorted.bam$")
>> RNASeq<- easyRNASeq(filesDirectory=getwd(),
>+                     organism="Hsapiens",
>+                     chr.sizes=chr.sizes,
>+                     #readLength=80L,
>+                     annotationMethod="biomaRt",
>+                     format="bam",
>+                     count="genes",
>+                     summarization="geneModels",
>+                     filenames=bamfiles[1],
>+                     outputFormat="RNAseq"
>+                     )
>
>
>
>Checking arguments...
>Fetching annotations...
>Computing gene models...
>Summarizing counts...
>Processing test.sorted.bam
>Updating the read length information.
>The reads have been trimmed.
>Minimum length of 50 bp.
>Maximum length of 80 bp.
>Error in mk_singleBracketReplacementValue(x, value) :
>  'value' must be a CompressedIntegerList object
>In addition: Warning messages:
>1: The use of the list for providing chromosome sizes has been
>deprecated.
>Use a named numeric vector instead.
>2: In easyRNASeq(filesDirectory = getwd(), organism = "Hsapiens",
>chr.sizes
>= chr.sizes,  :
>There are 16696 synthetic exons as determined from your annotation that
>overlap! This implies that some reads will be counted more than once!
>Is
>that really what you want?
>3: In fetchCoverage(rnaSeq, format = format, filename = filename,
>filter =
>filter,  :
>You enforce UCSC chromosome conventions, however the provided
>alignments
>are not compliant. Correcting it.
>4: In fetchCoverage(rnaSeq, format = format, filename = filename,
>filter =
>filter,  :
>Not all the chromosome names in your chromosome size list 'chr.sizes'
>are
>present in your read file(s) (aln or bam).
>5: In fetchCoverage(rnaSeq, format = format, filename = filename,
>filter =
>filter,  :
>  The available chromosomes in both your read file(s) (aln or bam) and
>'chr.sizes' list were restricted to their common term.
>These are: chr1, chr10, chr11, chr12, chr13, chr14, chr15, chr16,
>chr17,
>chr18, chr19, chr2, chr20, chr21, chr22, chr3, chr4, chr5, chr6, chr7,
>chr8, chr9, chrM, chrX, chrY.
>
>> sessionInfo()
>R version 2.15.1 (2012-06-22)
>Platform: x86_64-unknown-linux-gnu (64-bit)
>
>locale:
>[1] C
>
>attached base packages:
>[1] parallel  stats     graphics  grDevices utils     datasets  methods
>[8] base
>
>other attached packages:
> [1] BSgenome.Hsapiens.UCSC.hg19_1.3.19 easyRNASeq_1.3.14
> [3] ShortRead_1.15.11                  latticeExtra_0.6-24
> [5] RColorBrewer_1.0-5                 Rsamtools_1.9.30
> [7] DESeq_1.9.14                       lattice_0.20-6
> [9] locfit_1.5-8                       BSgenome_1.25.8
>[11] GenomicRanges_1.9.65               Biostrings_2.25.12
>[13] IRanges_1.15.44                    edgeR_2.99.8
>[15] limma_3.12.1                       biomaRt_2.13.2
>[17] Biobase_2.17.7                     genomeIntervals_1.13.3
>[19] BiocGenerics_0.3.1                 intervals_0.13.3
>
>loaded via a namespace (and not attached):
> [1] AnnotationDbi_1.18.1 DBI_0.2-5            RCurl_1.91-1
> [4] RSQLite_0.11.1       XML_3.9-4            annotate_1.34.1
> [7] bitops_1.0-4.1       genefilter_1.38.0    geneplotter_1.35.1
>[10] grid_2.15.1          hwriter_1.3          splines_2.15.1
>[13] stats4_2.15.1        survival_2.36-14     xtable_1.7-0
>[16] zlibbioc_1.2.0
>
>
>
>
>On 21 September 2012 16:37, Nicolas Delhomme <delhomme@embl.de> wrote:
>
>> Hi Yanju,
>>
>> Would you be OK with uploading the file that creates the problem on
>my
>> dropbox? If that's OK, I'll send you a link to it. That would be best
>for
>> me to reproduce the error.
>>
>> Cheers,
>>
>> Nico
>>
>> ---------------------------------------------------------------
>> Nicolas Delhomme
>>
>> Genome Biology Computational Support
>>
>> European Molecular Biology Laboratory
>>
>> Tel: +49 6221 387 8310
>> Email: nicolas.delhomme@embl.de
>> Meyerhofstrasse 1 - Postfach 10.2209
>> 69102 Heidelberg, Germany
>> ---------------------------------------------------------------
>>
>>
>>
>>
>>
>> On Sep 21, 2012, at 4:32 PM, Yanju Zhang wrote:
>>
>> > Hi Nico
>> > As mentioned in SEQAnswers, I also encountered this problem:
>> > > "Error in mk_singleBracketReplacementValue(x, value) :
>> > > 'value' must be a CompressedIntegerList object"
>> >
>> > In my bam files, the reads are with different length.
>> >
>> > I am expecting the solution. If you need more information, please
>let me
>> know.
>> >
>> >
>> > Best wishes
>> > Yanju
>> >
>> >
>>
>>
>
>        [[alternative HTML version deleted]]
>
>
>
>------------------------------
>
>Message: 5
>Date: Fri, 21 Sep 2012 17:59:35 +0200
>From: Nicolas Delhomme <delhomme@embl.de>
>To: Nicolas Delhomme <delhomme@embl.de>
>Cc: Dadi Gao <dgao3450@uni.sydney.edu.au>, bioconductor@r-project.org
>Subject: Re: [BioC] Error of GTF Annotation in easyRNASeq
>Message-ID: <E8F88D62-00CA-45B9-97B9-6B8DFA8CC0A7@embl.de>
>Content-Type: text/plain; charset=us-ascii
>
>Hi Dadi,
>
>The error comes from a change of API that affects a package I depend
>upon. I've contacted the maintainer and will let you know once it gets
>fixed. I might take some time though (~ 1 week).
>
>Cheers,
>
>Nico
>
>---------------------------------------------------------------
>Nicolas Delhomme
>
>Genome Biology Computational Support
>
>European Molecular Biology Laboratory
>
>Tel: +49 6221 387 8310
>Email: nicolas.delhomme@embl.de
>Meyerhofstrasse 1 - Postfach 10.2209
>69102 Heidelberg, Germany
>---------------------------------------------------------------
>
>
>
>
>
>On Sep 21, 2012, at 10:26 AM, Nicolas Delhomme wrote:
>
>> Moreover, to make sure that this is not a package conflict can you
>please NOT load the library(RnaSeqTutorial). You do not need it to run
>easyRNASeq. So your script should read:
>>
>> library(easyRNASeq)
>> library(BSgenome.Mmusculus.UCSC.mm9)
>>
>> setwd("/home/gao/RNA")
>>
>> ## the "." is your current directory.
>> count.table <- easyRNASeq(".",
>> pattern=".sorted.bam$",
>> organism="MMusculus",
>> annotationMethod="gtf",
>> annotationFile="mm9gene.gtf",
>> count="genes",
>> summarization="geneModels",
>> normalize=TRUE
>> )
>>
>>
>> Cheers,
>>
>> Nico
>>
>> ---------------------------------------------------------------
>> Nicolas Delhomme
>>
>> Genome Biology Computational Support
>>
>> European Molecular Biology Laboratory
>>
>> Tel: +49 6221 387 8310
>> Email: nicolas.delhomme@embl.de
>> Meyerhofstrasse 1 - Postfach 10.2209
>> 69102 Heidelberg, Germany
>> ---------------------------------------------------------------
>>
>>
>>
>>
>>
>> On Sep 21, 2012, at 10:19 AM, Nicolas Delhomme wrote:
>>
>>> Dear Dadi,
>>>
>>> I will need a little more information from you. In addition, it's
>best if you post such emails to the bioconductor mailing list (which
>I've Cced, so please "answer to all" when you reply.). See there for
>subscribing: http://www.bioconductor.org/help/mailing-list/. What I
>need to know from you first is what is described in that page:
>http://www.bioconductor.org/help/mailing-list/posting-guide/ mainly
>under the sections preparing and composing. In essence I need to know
>what version of R and bioconductor packages you are using.
>>>
>>> Then, installing you package in the installation directory of an
>existing package is not the safest. You might a) disrupt that package
>functionality b) possibly lose your data if that package gets updated.
>You'd rather move your RNA folder to you home directory and use that
>directory, e.g. /home/gao/RNA instead. Using the setwd command, you can
>make that your current working dir.
>>>
>>> So the following two blocks results in the same:
>>>
>>> setwd("/home/gao/RNA")
>>>
>>> ## the "." is your current directory.
>>> count.table <- easyRNASeq(".",
>>> pattern=".sorted.bam$",
>>> organism="MMusculus",
>>> annotationMethod="gtf",
>>> annotationFile="mm9gene.gtf",
>>> count="genes",
>>> summarization="geneModels",
>>> normalize=TRUE
>>> )
>>>
>>> Or:
>>>
>>> count.table <- easyRNASeq("/home/gao/RNA",
>>> pattern=".sorted.bam$",
>>> organism="MMusculus",
>>> annotationMethod="gtf",
>>> annotationFile="/home/gao/RNA /mm9gene.gtf",
>>> count="genes",
>>> summarization="geneModels",
>>> normalize=TRUE
>>> )
>>>
>>> Now, for the error, can you please tell me more about what aligner
>you used for you data , whether it is Paired-End or not and finally
>whether the reads have been dynamically trimmed (i.e. if reads of
>variable length are expected ) or not?
>>>
>>> What actually bothers me in your error is that it mentions:
>>>
>>> easyRNASeq(system.file("miRNA", package = "RnaSeqTutorial"),
>>>
>>> instead of
>>>
>>> easyRNASeq(system.file("RNA", package="RnaSeqTutorial"),
>>>
>>> i.e. miRNA instead of RNA. So to make sure that the error is
>reproducible can you move your RNA folder to a different directory and
>re-run the command as above? I don't expect this to solve the error
>though, but at least we'd have a "cleaner" setup for reproducing it.
>>>
>>> Best,
>>>
>>> Nico
>>>
>>> ---------------------------------------------------------------
>>> Nicolas Delhomme
>>>
>>> Genome Biology Computational Support
>>>
>>> European Molecular Biology Laboratory
>>>
>>> Tel: +49 6221 387 8310
>>> Email: nicolas.delhomme@embl.de
>>> Meyerhofstrasse 1 - Postfach 10.2209
>>> 69102 Heidelberg, Germany
>>> ---------------------------------------------------------------
>>>
>>>
>>>
>>>
>>>
>>> On Sep 21, 2012, at 2:41 AM, Dadi Gao wrote:
>>>
>>>> Dear Dr. Delhomme,
>>>>
>>>> I'm currently study gene expression pattern from deep sequencing
>data of mouse blood cell using easyRNASeq.
>>>> I created a folder called "RNA" under R package RnaSeqTutorial
>path.
>>>> Within this folder, I put 3 RNA-seq data files called
>"N1.sorted.bam", "N2.sorted.bam" and "N3.sorted.bam", with their bam
>index files.
>>>> It also contains a GTF file for mouse gene annotation downloaded
>from UCSC, called "mm9gene.gtf".
>>>>
>>>> I'm using the following code to normalize the gene expression:
>>>>
>>>> library(easyRNASeq)
>>>> library(RnaSeqTutorial)
>>>> library(BSgenome.Mmusculus.UCSC.mm9)
>>>>
>>>> count.table <- easyRNASeq(system.file("RNA",
>package="RnaSeqTutorial"),
>>>> pattern=".sorted.bam$",
>>>> organism="MMusculus",
>>>> annotationMethod="gtf",
>>>> annotationFile=system.file("RNA", "mm9gene.gtf",
>package="RnaSeqTutorial"),
>>>> count="genes",
>>>> summarization="geneModels",
>>>> normalize=TRUE
>>>> )
>>>>
>>>> But this runs with an error as:
>>>>
>>>> Checking arguments...
>>>> Fetching annotations...
>>>> Read 962651 records
>>>> Warning message:
>>>> In easyRNASeq(system.file("miRNA", package = "RnaSeqTutorial"),  :
>>>> You enforce UCSC chromosome conventions, however the provided
>chromosome size list is not compliant. Correcting it.
>>>> Error in all.annotation[all.annotation$type %in% annotation.type, ]
>:
>>>> error in evaluating the argument 'i' in selecting a method for
>function '[': Error in all.annotation$type %in% annotation.type :
>>>> error in evaluating the argument 'x' in selecting a method for
>function '%in%': Error in function (classes, fdef, mtable)  :
>>>> unable to find an inherited method for function "annotation", for
>signature "Genome_intervals_stranded"
>>>>
>>>> Did I do something wrong?
>>>>
>>>> Sincerely yours,
>>>> Dadi Gao
>>>>
>>>> Bioinformatics Group
>>>> Centenary Institute
>>>> Building 93, Royal Prince Alfred Hospital
>>>> Missenden Rd, Camperdown, NSW 2050
>>>> Australia
>>>>
>>>
>>> _______________________________________________
>>> Bioconductor mailing list
>>> Bioconductor@r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>> Search the archives:
>http://news.gmane.org/gmane.science.biology.informatics.conductor
>>
>
>
>
>------------------------------
>
>Message: 6
>Date: Fri, 21 Sep 2012 13:51:54 -0400
>From: Sean Davis <sdavis2@mail.nih.gov>
>To: bioconductor@r-project.org
>Subject: [BioC] Feature request in readVcf
>Message-ID:
>   <CANeAVBmmjpjryjx8AXVcDSD1XW4QbaJD=s7b3OaeP_Ypr-MxwA@mail.gmail.com>
>Content-Type: text/plain
>
>Hi, Val.
>
>Is there in interest in simply ignoring unknown INFO and GENOTYPE
>fields
>when parsing VCF files, perhaps by issuing a warning instead of an
>error?
>There are LOTS of malformed VCF files out there.  In some cases, they
>are
>not useable, but in this case, they can be perfectly useable if these
>unknown fields are simply ignored.
>
>> dat = readVcf('tmp.gatk.vcf',genome='hg19')
>Error: scanVcf: record 22 INFO 'KGPilot123' not found
>  path:
>/Volumes/CCRBioinfo/projects/RosenbergImmuneStudy/staging/tmp.gatk.vcf
>
>Thanks,
>Sean
>
>        [[alternative HTML version deleted]]
>
>
>
>------------------------------
>
>Message: 7
>Date: Fri, 21 Sep 2012 13:50:29 -0700
>From: "Tim Triche, Jr." <tim.triche@gmail.com>
>To: Sean Davis <sdavis2@mail.nih.gov>
>Cc: bioconductor@r-project.org
>Subject: Re: [BioC] Feature request in readVcf
>Message-ID:
>   <CAC+N9BVynUa_sMPcsFWWxMMu3ovzqNc314bQ6+C=eyEOzmGPMw@mail.gmail.com>
>Content-Type: text/plain
>
>+1
>
>thanks,
>
>--t
>
>
>
>On Fri, Sep 21, 2012 at 10:51 AM, Sean Davis <sdavis2@mail.nih.gov>
>wrote:
>
>> Hi, Val.
>>
>> Is there in interest in simply ignoring unknown INFO and GENOTYPE
>fields
>> when parsing VCF files, perhaps by issuing a warning instead of an
>error?
>>  There are LOTS of malformed VCF files out there.  In some cases,
>they are
>> not useable, but in this case, they can be perfectly useable if these
>> unknown fields are simply ignored.
>>
>> > dat = readVcf('tmp.gatk.vcf',genome='hg19')
>> Error: scanVcf: record 22 INFO 'KGPilot123' not found
>>   path:
>>
>/Volumes/CCRBioinfo/projects/RosenbergImmuneStudy/staging/tmp.gatk.vcf
>>
>> Thanks,
>> Sean
>>
>>         [[alternative HTML version deleted]]
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor@r-project.org
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives:
>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>
>
>
>
>--
>*A model is a lie that helps you see the truth.*
>*
>*
>Howard
>Skipper<http://cancerres.aacrjournals.org/content/31/9/1173.full.pdf>
>
>        [[alternative HTML version deleted]]
>
>
>
>------------------------------
>
>Message: 8
>Date: Fri, 21 Sep 2012 17:49:26 -0700
>From: Marc Carlson <mcarlson@fhcrc.org>
>To: bioconductor@r-project.org
>Subject: Re: [BioC] GO annotation
>Message-ID: <505D0B16.80804@fhcrc.org>
>Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>Hi Lim,
>
>First of all it all depends on what you have for gene identifiers.  If
>you are like most people you will have entrez gene IDs.  So for now I
>will assume you have those.
>
>## So lets further assume you are working with humans and just choose
>the 1st two entrez gene IDs so that we can make a (hopefully
>meaningful)
>example
>ids = c("1","2")
>## now load the org library for humans
>library(org.Hs.eg.db)
>## then you can call select to extract your GO IDs like this:
>select(org.Hs.eg.db, keys = ids, cols = "GO", keytype = "ENTREZID")
>
>Now one thing to notice is that if you have some other kind of
>identifier, then your keytype argument will have to be set to a
>different value.  And hopefully, the kind of ID you are using, is
>present in the package that you have to search...  See the manual page
>for select for more information.
>
>?select
>
> From your question, I also recognize that you may not be able to do
>this because it sounds like you might be using a more unusual organism
>and not be using something commonplace like human.  Well don't give up
>just yet, because we may be able to help you there too.  You can look
>at
>the manual page for the function makeOrgPackageFromNCBI to learn how
>you
>can try to generate an org package from just the taxonomy ID (which you
>can look up on NCBIs website).  If the data is available at NCBI, then
>you should be able to generate a package from NCBI that will match your
>organism of choice.
>
>?makeOrgPackageFromNCBI
>
>
>Does that answer your question?
>
>
>   Marc
>
>
>
>On 09/21/2012 02:35 AM, KJ Lim wrote:
>> Dear Bioconductor community,
>>
>> Good day.
>>
>> I did the differential expression analysis for my RNA-Seq data with
>edgeR
>> package. I have a list of differentially expressed genes now and I
>would
>> like to find the GO terms for the genes.
>>
>> I have been reading and searching around for the right package. But,
>I
>> found that several packages are developed based on model species.
>Could the
>> community kindly please suggest me what GO annotation package I can
>use for
>> non-model species; plant RNA-Seq data?
>>
>> Thank you very much and have a nice weekend.
>>
>> Best regards,
>> KJ Lim
>>
>>       [[alternative HTML version deleted]]
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor@r-project.org
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives:
>http://news.gmane.org/gmane.science.biology.informatics.conductor
>
>
>
>------------------------------
>
>Message: 9
>Date: Sat, 22 Sep 2012 01:21:29 -0400
>From: "Srinivasan, Sathish  K" <SSrinivasan@med.miami.edu>
>To: Marc Carlson <mcarlson@fhcrc.org>, "bioconductor@r-project.org"
>        <bioconductor@r-project.org>
>Subject: Re: [BioC] GO annotation
>Message-ID:
><4EB41664F8279A4CA870A740E038CFEA3E1E7EB0CB@MEDEXMB05.ad.med.miami.edu>
>
>Content-Type: text/plain; charset="us-ascii"
>
>Hi Marc,
>Could you suggest a go-to literature reference on annotating genomic
>data using bioconductor packages, probably a book or any of its kind.
>Thanks
>
>~Sathish
>
>-----Original Message-----
>From: bioconductor-bounces@r-project.org
>[mailto:bioconductor-bounces@r-project.org] On Behalf Of Marc Carlson
>Sent: Friday, September 21, 2012 8:49 PM
>To: bioconductor@r-project.org
>Subject: Re: [BioC] GO annotation
>
>Hi Lim,
>
>First of all it all depends on what you have for gene identifiers.  If
>you are like most people you will have entrez gene IDs.  So for now I
>will assume you have those.
>
>## So lets further assume you are working with humans and just choose
>the 1st two entrez gene IDs so that we can make a (hopefully
>meaningful) example ids = c("1","2") ## now load the org library for
>humans
>library(org.Hs.eg.db)
>## then you can call select to extract your GO IDs like this:
>select(org.Hs.eg.db, keys = ids, cols = "GO", keytype = "ENTREZID")
>
>Now one thing to notice is that if you have some other kind of
>identifier, then your keytype argument will have to be set to a
>different value.  And hopefully, the kind of ID you are using, is
>present in the package that you have to search...  See the manual page
>for select for more information.
>
>?select
>
>From your question, I also recognize that you may not be able to do
>this because it sounds like you might be using a more unusual organism
>and not be using something commonplace like human.  Well don't give up
>just yet, because we may be able to help you there too.  You can look
>at the manual page for the function makeOrgPackageFromNCBI to learn how
>you can try to generate an org package from just the taxonomy ID (which
>you can look up on NCBIs website).  If the data is available at NCBI,
>then you should be able to generate a package from NCBI that will match
>your organism of choice.
>
>?makeOrgPackageFromNCBI
>
>
>Does that answer your question?
>
>
>   Marc
>
>
>
>On 09/21/2012 02:35 AM, KJ Lim wrote:
>> Dear Bioconductor community,
>>
>> Good day.
>>
>> I did the differential expression analysis for my RNA-Seq data with
>> edgeR package. I have a list of differentially expressed genes now
>and
>> I would like to find the GO terms for the genes.
>>
>> I have been reading and searching around for the right package. But,
>I
>> found that several packages are developed based on model species.
>> Could the community kindly please suggest me what GO annotation
>> package I can use for non-model species; plant RNA-Seq data?
>>
>> Thank you very much and have a nice weekend.
>>
>> Best regards,
>> KJ Lim
>>
>>       [[alternative HTML version deleted]]
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor@r-project.org
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives:
>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>
>_______________________________________________
>Bioconductor mailing list
>Bioconductor@r-project.org
>https://stat.ethz.ch/mailman/listinfo/bioconductor
>Search the archives:
>http://news.gmane.org/gmane.science.biology.informatics.conductor
>
>
>
>------------------------------
>
>Message: 10
>Date: Sat, 22 Sep 2012 00:23:09 +0200
>From: Daniela Lopes Paim Pinto <d.lopespaimpinto@sssup.it>
>To: bioconductor@r-project.org
>Subject: [BioC] Is normalization in edgeR required for small RNA
>        sequencing      data?
>Message-ID:
>   <CAHk-rA1aW+TCnkAjrAX7wfJYcHH22WHN2SfwHat2wMU-=WWdsA@mail.gmail.com>
>Content-Type: text/plain
>
>Dear All,
>
>I am PhD student, currently working on differential expression analysis
>of
>my smallRNA library deep sequencing data and trying to identify
>differentially expressed miRNAs, using edgeR package. I have 24
>different
>samples with 2 biological replicates (48 libraries).  I am performing
>multiple group comparison using GLM method and also Anova-like test to
>idetify DE miRNAs among the different groups of my samples.
>My question is :
>
>Do  I need to normalize my input data using *calcNormFactors() *once I
>set
>my DGE list or I could  proceed without any normalization? I assume in
>this
>case that edgeR  performs a default normallization when it  is
>"calculating
>library sizes from column totals"?
>
>
>I would really appreciate any suggestion on this!
>
>
>Thanks in advance,
>
>
>Daniela
>
>        [[alternative HTML version deleted]]
>
>
>
>------------------------------
>
>Message: 11
>Date: Sat, 22 Sep 2012 08:03:32 +0100
>From: Jill Pleasance <jpleasance@gmail.com>
>To: bioconductor@r-project.org
>Subject: [BioC] NGS public data analysis
>Message-ID:
>   <CAJhs7Oj_eBg2VgBX=FPYvXxKBDq-tdzZmDBmSYMNAU=r6Gp6Lw@mail.gmail.com>
>Content-Type: text/plain
>
>Hi
>
>
>
>I am writing as I am trying to analyse NGS data from public data (GEO)
>specifically datasets such as one sample per time point.  The raw
>(somewhat
>processed data) is 3 samples at different time points where ?The read
>count
>at exon, splice-junction, transcript and gene levels were summarized
>and
>normalized to relative abundance in Fragments Per Kilobase of exon
>model
>per Million (FPKM) in order to compare transcription level among
>samples.?
>
>
>
>The authors of this paper then used The differentially expressed
>transcripts were identified using M-A based random sampling method
>implemented in DEGseq package in BioConductor (
>http://bioconductor.org/packages/2.5/bioc/html/DEGseq.html). The
>transcripts were further filtered at > 2-fold change and a minimum read
>count of 50 in either condition.
>
>
>
>I have read through some of your posts where Gordon suggested using a
>simple excel formula to achieve fold changes when you don?t have
>replicates
>
>*lib.size1 <- sum(y1)*
>
>>>*   lib.size2 <- sum(y2)*
>
>>>*   logFC <- log2((y1+0.5)/(lib.size1+0.5)/(y2+0.5)*(lib.size2+0.5))*
>
>* *
>
>Is this something I could apply to the current analysis?  I have 3
>files -
>with gene ID and counts (one for each sample) and if genes are not
>listed
>in the sample files ? I assume the counts are zero.  Would you have any
>suggestions as to what to do with these zero count reads?
>
>
>I am trying to avoid learning how to script write at the moment to see
>if
>this analysis works and obviously when

--
Sent from my Android phone with K-9 Mail. Please excuse my brevity.
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