Bimodal Distrinbution
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@francesco-mancuso-3183
Last seen 10.2 years ago
Hi all! I'm a little newbie with R... I'm working with quantitative proteomics data that have a bimodal distribution. For you what is the best function to work with this type of data? Thanks in advance! Francesco -- *Francesco Mattia Mancuso* /Proteomics and Functional Genomics Group/ http://www.ifom-ieo-campus.it/research/bonaldi.php /Mass Spectrometry Unit/ http://www.ifom-ieo-campus.it/services/masspectrometry.php European Institute of Oncology Via Adamello 16 - 20139 Milano [Ph] +39-02-94375102 [email] francesco.mancuso@ifom-ieo-campus.it <mailto:francesco.mancuso@ifom-ieo-campus.it> [[alternative HTML version deleted]]
Proteomics Proteomics • 1.8k views
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@sean-davis-490
Last seen 3 months ago
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On Tue, Dec 9, 2008 at 1:19 PM, Francesco Mancuso <francesco.mancuso at="" ifom-ieo-campus.it=""> wrote: > Hi all! > I'm a little newbie with R... > > I'm working with quantitative proteomics data that have a bimodal > distribution. > For you what is the best function to work with this type of data? Hi, Francesco. What do you want to do with the data? Are you looking for differential expression? Trying to normalize data? Sean
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Hi Sean! Everything...but principally what you said. I have to normalize data, then to look for "differential express" protein and calculate a p-value of how much the outliers differs from median. Finally I have to map a set of proteins into the distribution to understand if they are over-expressed in a mutant proteome. Thanks! Francesco Sean Davis wrote: > On Tue, Dec 9, 2008 at 1:19 PM, Francesco Mancuso > <francesco.mancuso@ifom-ieo-campus.it> wrote: > >> Hi all! >> I'm a little newbie with R... >> >> I'm working with quantitative proteomics data that have a bimodal >> distribution. >> For you what is the best function to work with this type of data? >> > > Hi, Francesco. > > What do you want to do with the data? Are you looking for > differential expression? Trying to normalize data? > > Sean > -- *Francesco Mattia Mancuso* Bioinformatician /Proteomics and Functional Genomics Group/ http://www.ifom-ieo-campus.it/research/bonaldi.php /Mass Spectrometry Unit/ http://www.ifom-ieo-campus.it/services/masspectrometry.php European Institute of Oncology Via Adamello 16 - 20139 Milano [Ph] +39-02-94375102 [email] francesco.mancuso@ifom-ieo-campus.it <mailto:francesco.mancuso@ifom-ieo-campus.it> [[alternative HTML version deleted]]
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Sorry, Francesco. You'll probably need to provide some more detail. We don't even know whether you have mass-spec data, protein arrays, IHC, or some other assay. Perhaps there is a package in Bioconductor that can help, but you'll have to give folks a bit more to work with to figure that out. Sean On Tue, Dec 9, 2008 at 2:12 PM, Francesco Mancuso <francesco.mancuso at="" ifom-ieo-campus.it=""> wrote: > Hi Sean! > Everything...but principally what you said. > I have to normalize data, then to look for "differential express" > protein and calculate a p-value of how much the outliers differs from > median. > Finally I have to map a set of proteins into the distribution to > understand if they are over-expressed in a mutant proteome. > Thanks! > Francesco > > Sean Davis wrote: >> On Tue, Dec 9, 2008 at 1:19 PM, Francesco Mancuso >> <francesco.mancuso at="" ifom-ieo-campus.it=""> wrote: >> >>> Hi all! >>> I'm a little newbie with R... >>> >>> I'm working with quantitative proteomics data that have a bimodal >>> distribution. >>> For you what is the best function to work with this type of data? >>> >> >> Hi, Francesco. >> >> What do you want to do with the data? Are you looking for >> differential expression? Trying to normalize data? >> >> Sean >> > > -- > *Francesco Mattia Mancuso* > Bioinformatician > > /Proteomics and Functional Genomics Group/ > http://www.ifom-ieo-campus.it/research/bonaldi.php > > /Mass Spectrometry Unit/ > http://www.ifom-ieo-campus.it/services/masspectrometry.php > > European Institute of Oncology > Via Adamello 16 - 20139 Milano > [Ph] +39-02-94375102 > [email] francesco.mancuso at ifom-ieo-campus.it > <mailto:francesco.mancuso at="" ifom-ieo-campus.it=""> > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >
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Hi, there is probably a very simple answer to this question but why does the following code produce the output NULL? ensembl = useMart("ensembl", dataset="hsapiens_gene_ensembl") getBM(attributes = c("entrezgene", "hgnc_symbol"), filters = "entrezgene", values = "117581", mart = ensembl, na.value = NA) The NCBI site has a hgnc symbol listed for the gene: http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=Retrieve&dopt=Gra phics&list_uids=117581 thanks, Sebastien
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On Tue, Dec 9, 2008 at 7:21 PM, Sebastien Gerega <seb at="" gerega.net=""> wrote: > Hi, > there is probably a very simple answer to this question but why does the > following code produce the output NULL? > > ensembl = useMart("ensembl", dataset="hsapiens_gene_ensembl") > getBM(attributes = c("entrezgene", "hgnc_symbol"), filters = "entrezgene", > values = "117581", mart = ensembl, na.value = NA) > > The NCBI site has a hgnc symbol listed for the gene: > http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=Retrieve&dopt=G raphics&list_uids=117581 If you do a similar search at Ensembl, it appears that Ensembl does not have an entry for TWIST2. (I did the search quickly, so I could be mistaken.) Remember that these genome databases do not always agree about what a gene represents (or even which ones exist). Sean
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I thought that might be the case, I was just surprised by how many genes didn't show up in Ensembl.... Sean Davis wrote: > On Tue, Dec 9, 2008 at 7:21 PM, Sebastien Gerega <seb at="" gerega.net=""> wrote: > >> Hi, >> there is probably a very simple answer to this question but why does the >> following code produce the output NULL? >> >> ensembl = useMart("ensembl", dataset="hsapiens_gene_ensembl") >> getBM(attributes = c("entrezgene", "hgnc_symbol"), filters = "entrezgene", >> values = "117581", mart = ensembl, na.value = NA) >> >> The NCBI site has a hgnc symbol listed for the gene: >> http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=Retrieve&dopt= Graphics&list_uids=117581 >> > > If you do a similar search at Ensembl, it appears that Ensembl does > not have an entry for TWIST2. (I did the search quickly, so I could > be mistaken.) Remember that these genome databases do not always > agree about what a gene represents (or even which ones exist). > > Sean > >
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Dear Sebastian thank you. This is turning not really to be a "biomaRt" (the R package) question, but one for "Ensembl" (the online database). I think they'd be happy to hear your feedback (including all the other many genes you mention)! Go to Ensembl http://www.ensembl.org/info/website/help and select "contact helpdesk". I did find "TWIST2" in Ensembl, but apparently the association with the EntrezGene ID is not present in all datasets produced by the Biomart database warehouse. Best wishes Wolfgang ---------------------------------------------------- Wolfgang Huber, EMBL-EBI, http://www.ebi.ac.uk/huber Sebastien Gerega ha scritto: > I thought that might be the case, I was just surprised by how many genes > didn't show up in Ensembl.... > > Sean Davis wrote: >> On Tue, Dec 9, 2008 at 7:21 PM, Sebastien Gerega <seb at="" gerega.net=""> wrote: >> >>> Hi, >>> there is probably a very simple answer to this question but why does the >>> following code produce the output NULL? >>> >>> ensembl = useMart("ensembl", dataset="hsapiens_gene_ensembl") >>> getBM(attributes = c("entrezgene", "hgnc_symbol"), filters = >>> "entrezgene", >>> values = "117581", mart = ensembl, na.value = NA) >>> >>> The NCBI site has a hgnc symbol listed for the gene: >>> http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=Retrieve&dopt =Graphics&list_uids=117581 >>> >>> >> >> If you do a similar search at Ensembl, it appears that Ensembl does >> not have an entry for TWIST2. (I did the search quickly, so I could >> be mistaken.) Remember that these genome databases do not always >> agree about what a gene represents (or even which ones exist). >> >> Sean >>
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@mayer-claus-dieter-3184
Last seen 10.2 years ago
Hi Francesco! You are not very specific about what you mean by bimodal distribution, but I assume that you mean the distribution across ALL proteins. This would suggest that you can roughly classify your measurements into two groups: small ones (mode1) and large ones (mode2). It wouldn't have direct implications though if you want to find differentially expressed proteins, because there you only compare the values for the same protein. So for example the aim of a normalization would not be to remove the bi-modality but to make sure that the bi-modal distribution is more or less the same for each sample (at least for the non-changing proteins). Claus -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor- bounces@stat.math.ethz.ch] On Behalf Of Francesco Mancuso Sent: 09 December 2008 18:19 To: bioconductor at stat.math.ethz.ch Subject: [BioC] Bimodal Distrinbution Hi all! I'm a little newbie with R... I'm working with quantitative proteomics data that have a bimodal distribution. For you what is the best function to work with this type of data? Thanks in advance! Francesco -- *Francesco Mattia Mancuso* /Proteomics and Functional Genomics Group/ http://www.ifom-ieo-campus.it/research/bonaldi.php /Mass Spectrometry Unit/ http://www.ifom-ieo-campus.it/services/masspectrometry.php European Institute of Oncology Via Adamello 16 - 20139 Milano [Ph] +39-02-94375102 [email] francesco.mancuso at ifom-ieo-campus.it <mailto:francesco.mancuso at="" ifom-ieo-campus.it=""> [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor The University of Aberdeen is a charity registered in Scotland, No SC013683.
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