how to map Affymetrix ID to ensemble gene ID
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wang peter ★ 2.0k
@wang-peter-4647
Last seen 10.2 years ago
DEAR all: i have some Affymetrix ID from GeneChip Porcine Genome Array i want to map them to ensemble gene ID or other gene id for analysis can u tell me why package can be used to do so? thank you very much -- shan gao Room 231(Dr.Fei lab) Boyce Thompson Institute Cornell University Tower Road, Ithaca, NY 14853-1801 Office phone: 1-607-254-1267(day) Official email:sg839 at cornell.edu Facebook:http://www.facebook.com/profile.php?id=100001986532253
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@sean-davis-490
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United States
On Sun, Mar 18, 2012 at 10:05 AM, wang peter <wng.peter@gmail.com> wrote: > DEAR all: > i have some Affymetrix ID from GeneChip Porcine Genome Array > i want to map them to ensemble gene ID or other gene id for analysis > can u tell me why package can be used to do so? > For everything related to Ensembl, the first stop is biomaRt. In this particular case, I am pretty sure that Ensembl maps to the Porcine genechip. Sean [[alternative HTML version deleted]]
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Hello I tried to the copyCountSegments from exomeCopy, but it failed as shown below. It complained negative width, but I table the width value, and have never found any negative value in width column for range objects. Could any one give some suggestions? Thanks. John > fit <- exomeCopy(exomecounts["chr1"],sample.name="HGPIPE_6159", +                    X.names=c("bg","GC","GC.sq","width"),S=0:6,d=2) >   show(fit) ExomeCopy object type: exomeCopy percent normal state: 100% > copyCountSegments(fit) Error in .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges") :   solving row 1: negative widths are not allowed > sessionInfo() R version 2.14.2 (2012-02-29) Platform: x86_64-unknown-linux-gnu (64-bit) locale:  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8  [7] LC_PAPER=C                 LC_NAME=C  [9] LC_ADDRESS=C               LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats     graphics  grDevices utils     datasets  methods   base other attached packages: [1] exomeCopy_1.0.2     Rsamtools_1.6.3     Biostrings_2.22.0 [4] GenomicRanges_1.6.7 IRanges_1.12.6      foreign_0.8-49 loaded via a namespace (and not attached): [1] bitops_1.0-4.1     BSgenome_1.22.0    RCurl_1.91-1 rtracklayer_1.14.4 [5] tools_2.14.2       XML_3.9-4          zlibbioc_1.0.1 > [[alternative HTML version deleted]]
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dear Sean thank you for your reply but which function in biomart can be used to Ensembl maps to the Porcine genechip. -- shan gao Room 231(Dr.Fei lab) Boyce Thompson Institute Cornell University Tower Road, Ithaca, NY 14853-1801 Office phone: 1-607-254-1267(day) Official email:sg839 at cornell.edu Facebook:http://www.facebook.com/profile.php?id=100001986532253
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Hi Peter, On 03/18/2012 02:10 PM, wang peter wrote: > dear Sean > thank you for your reply > but which function in biomart can be used to Ensembl maps to the > Porcine genechip. Please do some home work e.g. read the vignette, look at the examples in the package etc... Let's try this: don't send a question to the list before you've spent at least 10 minutes trying to answer the question yourself. Even if you can't find the answer to your question after 10 minutes, you'll still learn a lot of useful things and get a better understanding of the tools you are trying to use. Thanks! H. > > > > > -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpages at fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319
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dear Hervé Pagès: thank you for your reply, but i donot think there are some people can find my answer in 10 mins. if you know who can, i will stop my research and feel ashamed and kill myself. anyway, i read the examples which said there is a getAffyArrays() ,but there is no. it mislead me and killed more than 10 min of me thank u. anyway, my case is special, it is pig microarray, not human, mouse -- shan gao Room 231(Dr.Fei lab) Boyce Thompson Institute Cornell University Tower Road, Ithaca, NY 14853-1801 Office phone: 1-607-254-1267(day) Official email:sg839 at cornell.edu Facebook:http://www.facebook.com/profile.php?id=100001986532253
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Dear Peter, I think you misunderstood Herv?'s answer. The point was not about doing your research in 10 minutes, but if you know someone that can do my research in ten minutes, I'd glad to hire him/her :-). The points were : 1) by looking in the documentation you'll learn more about these packages. It will always be helpful for you even if it does not give you the answer. It will give you a better understanding of the package functionality and help you describe your problem better. This is essential, you'll see next. 2) Sean already gave you an answer to that question, namely to look at the getBM() function. From your answer to his email, it seemed (note that I don't know what you did) that you had not investigated the matter much further. I say it "seemed" because you formulated your email almost exactly in the same way as your original one, demonstrating no progress in your thoughts about the problem. Again here I don't know what the truth is, I'm just saying how it came out. Now it is important to understand that the exchange on this list and especially the answers are given freely by people on their own time (I spend my 10+ mins answering you) so that it benefits all of us as a whole. I hope that you understand it is essential for the people asking questions to be concise, precise and respectful of the work of others. By showing progress in your problem consideration and suggesting new approaches, you would then elicit another answer and by this step-wise process you'll likely end up with a solution to your problem. It will cost you time, and to the people answering you too, but it is no lost time, because you'll get a solution in less time that it would have taken you to get it alone, plus it might benefit other list members. That is the spirit of this list and it needs to remain so, otherwise less and less people will be willing to answer questions and all of us will be on our own to solve our problems. Now to your problem; if the function you are looking for does not exists, you might have to write it on your own. The starting point is the getBM() function. You need first to connect to a mart database (look at the useMart, listMarts, listDataset functions) and then use the getBM() function using "filters" and "attributes" (look at the listAttributes and listFilters function) to retrieve the information about the affy probes you're interested in. Look at the biomaRt vignette for the details on that. Note that I was in the same situation as you three years ago and I made my way through the vignette to get to my solution. R and Bioconductor do have a lot of documentation and reading it is no loss of time, I hope I made that clear. Finally, if the getAffyArrays function does not exist but is stated in the documentation, then you need to report that in your original email. The more you explain, the more likely you are to get a quick answer. HTH, Nico --------------------------------------------------------------- Nicolas Delhomme Genome Biology Computational Support European Molecular Biology Laboratory Tel: +49 6221 387 8310 Email: nicolas.delhomme at embl.de Meyerhofstrasse 1 - Postfach 10.2209 69102 Heidelberg, Germany --------------------------------------------------------------- On 18 Mar 2012, at 22:27, wang peter wrote: > dear Hervé Pagès: > thank you for your reply, but i donot think there are > some people can find my answer in 10 mins. if you know > who can, i will stop my research and feel ashamed and > kill myself. > anyway, i read the examples which said there is a > getAffyArrays() ,but there is no. it mislead me and killed > more than 10 min of me > thank u. anyway, my case is special, it is pig microarray, > not human, mouse > > > -- > shan gao > Room 231(Dr.Fei lab) > Boyce Thompson Institute > Cornell University > Tower Road, Ithaca, NY 14853-1801 > Office phone: 1-607-254-1267(day) > Official email:sg839 at cornell.edu > Facebook:http://www.facebook.com/profile.php?id=100001986532253 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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dear Nicolas Delhomme: thx for your teaching. i donot want to argue with you. but if i do, i would u like to argue with a person i respect a lot. so i do a little argue with u. first i am not peter, please see my name is shan gao. second, my quesiton is very clear and concise. third, my case is special, it is pig genome. i donot think i can use getBM() function using "filters" and "attributes" (look at the listAttributes and listFilters function) to finish my work. how can you and other people think i am not familiar with the Biomart package. i can use it very well, but it cannot solve my problem. and if all the people must read and solve the problem by themselves. why did they build this forum and mailling list? if somebody did the same work and others will do, that is really WASTE of time. thank you shan gao
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On Sun, Mar 18, 2012 at 6:29 PM, wang peter <wng.peter@gmail.com> wrote: > dear Nicolas Delhomme: > thx for your teaching. i donot want to argue with you. but > if i do, i would u like to argue with a person i respect a lot. > so i do a little argue with u. first i am not peter, please see > my name is shan gao. Your email address says otherwise, so you should expect some confusion. > second, my quesiton is very clear and > concise. third, my case is special, it is pig genome. i donot think > i can use getBM() function using "filters" and "attributes" (look at > the listAttributes and listFilters function) to finish my work. Please send the code that shows that the Sus scrofa genome is not represented in biomaRt. That will involve using the useMart() and listDatasets() functions. After you show that code and the result, we can have a better discussion. However, I think you might be surprised by the results you obtain. > how > can you > and other people think i am not familiar with the Biomart package. i can use it very well, but it cannot solve my problem. > We do not assume that you either do or do not know how to use the biomaRt package. We do SUGGEST STRONGLY, however, that when one of us suggests that you try something that you ACTUALLY DO IT. If, for some reason it does not work for you, show why it did not work or what, specifically, you did not understand. Also, we assume that you have read the relevant documentation carefully (every function or method that you use) and the onus is on you to show that you have. > and if all the people must read and solve the problem by themselves. > why did they build this forum and mailling list? I answered your question quite clearly, I believe. I did not do your work for you, though. There is a difference. Please do not take my remark here to be anything other than constructive. > if somebody did the same work and others will do, that is really > WASTE of time. > The purpose of the email list is NOT simply to have users simply share convenient code, although it sometimes serves that purpose. The email list is to help users HELP THEMSELVES to solve their specific problems; my writing code for you will help you in the short run, but not always in the long run. Also, keep in mind that all of us are busy people, so please do not expect worked code examples to be posted to the list, especially when the example in the documentation answers the question. Again, I hope you take both Nico and my comments in the most constructive way possible. All of us were in your shoes at one point and know that learning Bioconductor can be challenging. Sean [[alternative HTML version deleted]]
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Dear Shan Gao, Sorry for the name mistake, but your email come as that of "wang peter". Here is how I would you do: mart <- useMart("ensembl") listDatasets(mart) ## I suppose the 45th entry is what you want (Pig = Sus scrofa) listDatasets(mart)[45,] mart <- useDataset("sscrofa_gene_ensembl",mart) ## Here we get lucky at position 53 grep("affy",listAttributes(mart)[,1]) listAttributes(mart)[53,] ## So now you can do your getBM query to get your affy probeset and related information ## (well extend the command obviously with what you need) getBM("affy_porcine",mart) Note: 1) I did not know that dataset before 2) I've never retrieved affy IDs before that way, but I knew it was possible through my previous readings of the documentation 3) I like to argue with you too, so a) your question was actually too concise (the more details the better) b) precise in your email that you are familiar with biomaRt (it would avoid such answers as before, and get you useful ones). Just tell me how we could know from your posts that it was otherwise? c) post your code and where you're stuck d) as I said it's a step by step process. You have an issue, you post it with details, you get an answer, you work until the next problem, etc. e) Again as I said, it's my free time and free will to answer you. This list is made so that people do get help when they need, and it's a reciprocal process. Next time I have an issue, maybe you can help. And for that you would need as much info from me as possible, right? Anyway, I hope this helps. If that solution still does not give you the information you need, then post again on the list explaining in details why not and what you are looking for. Best, Nico > sessionInfo() R version 2.14.1 Patched (2011-12-23 r57982) Platform: i386-apple-darwin9.8.0/i386 (32-bit) locale: [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] biomaRt_2.10.0 loaded via a namespace (and not attached): [1] RCurl_1.9-5 tools_2.14.1 XML_3.9-2 --------------------------------------------------------------- Nicolas Delhomme Genome Biology Computational Support European Molecular Biology Laboratory Tel: +49 6221 387 8310 Email: nicolas.delhomme at embl.de Meyerhofstrasse 1 - Postfach 10.2209 69102 Heidelberg, Germany --------------------------------------------------------------- On 18 Mar 2012, at 23:29, wang peter wrote: > dear Nicolas Delhomme: > thx for your teaching. i donot want to argue with you. but > if i do, i would u like to argue with a person i respect a lot. > so i do a little argue with u. first i am not peter, please see > my name is shan gao. second, my quesiton is very clear and > concise. third, my case is special, it is pig genome. i donot think > i can use getBM() function using "filters" and "attributes" (look at > the listAttributes and listFilters function) to finish my work. how > can you > and other people think i am not familiar with the Biomart package. > i can use it very well, but it cannot solve my problem. > and if all the people must read and solve the problem by themselves. > why did they build this forum and mailling list? > if somebody did the same work and others will do, that is really > WASTE of time. > > thank you > shan gao
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Dear Shan Gao, Perhaps you can try this: >ensembl <- useMart("ensembl", data = "sscrofa_gene_ensembl") >filters <- listFilters(ensembl) Looking through filters for anything related to affymetrix yields this: > filters[grep("Affy",filters$description),] name description 9 with_affy_porcine with Affy Porcine probeset ID(s) 62 affy_porcine Affy Porcine probeset ID(s) [e.g. Ssc.25128.1.S1_at] Now, try to read up on the example just before section 4 in the biomaRt vigenette. Best, David Westergaard 2012/3/18 wang peter <wng.peter at="" gmail.com="">: > dear Nicolas Delhomme: > ? ? ? ?thx for your teaching. i donot want to argue with you. but > if i do, i would u like to argue with a person i respect a lot. > ? ? ? ?so i do a little argue with u. first i am not peter, please see > my name is shan gao. ?second, my quesiton is very clear and > concise. third, my case is special, it is pig genome. i donot think > i can use getBM() function using "filters" and "attributes" (look at > the listAttributes and listFilters function) to finish my work. how > can you > and other people think i am not familiar with the Biomart package. > i can use it very well, but it cannot solve my problem. > ? ? ? ?and if all the people must read and solve the problem by themselves. > why did they build this forum and mailling list? > ? ? ? ?if somebody did the same work and others will do, that is really > WASTE of time. > > thank ?you > shan gao > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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On Sun, Mar 18, 2012 at 5:10 PM, wang peter <wng.peter@gmail.com> wrote: > dear Sean > thank you for your reply > but which function in biomart can be used to Ensembl maps to the > Porcine genechip. > > I'm sorry if my last email did not make it to you. Look at the getBM() function. Sean [[alternative HTML version deleted]]
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@david-westergaard-5119
Last seen 10.2 years ago
Hello, I guess you would use the http://www.bioconductor.org/packages/release/data/annotation/html/porc ine.db.html package, you can read more about the functions in the vignette http://www.bioconductor.org/packages/release/data/annotation/manuals/p orcine.db/man/porcine.db.pdf If that doesn't suit your needs, you'll have to manually parse the annotation file available from Affymetrix, though that requires a login. Best regards, David Westergaard 2012/3/18 wang peter <wng.peter at="" gmail.com="">: > DEAR all: > i have some Affymetrix ID from GeneChip Porcine Genome Array > i want to map them to ensemble gene ID or other gene id for analysis > can u tell me why package can be used to do so? > thank you very much > > -- > shan gao > Room 231(Dr.Fei lab) > Boyce Thompson Institute > Cornell University > Tower Road, Ithaca, NY 14853-1801 > Office phone: 1-607-254-1267(day) > Official email:sg839 at cornell.edu > Facebook:http://www.facebook.com/profile.php?id=100001986532253 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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