webbioc chicken
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jane janes ▴ 20
@jane-janes-2049
Last seen 8.1 years ago
Dear List, Recently I installed webbioc on my laptop. It works perfect but our lab is interested mainly in chicken affymetrix microarray analysis. (I can use affy and multtest with our chicken affy CEL files but no further analysis is possible.) I have some perl programming experience and almost no R. Nevertheless I Installed all the chicken related packages I found on the bioconductor web site (like chickencdf, chickenprobe, ggahomolgy etc) and I tried to make webbioc (annaffy) to work with them by modifying the cgi scripts. The only output I have been able to acquire was HTML table containing links to the affymetrix probe description webpages. I understand that the R packages behind the webbioc interface must be supplied with the correctly formated microarray data packages to work properly but most probably I have been unable to identify the right files in the bioconductor repository. Here are and my questions: Do such affy chicken files (correctly formatted for webbioc) exist? If they do not exist is it possible to be created by using the already available R modules and packages? Please excuse me if my question is not very well structured but I am relatively new recruit in the world of R and bioinformatics. Thank you very much in advance for your answers. Vassil
Microarray cdf probe multtest affy webbioc Microarray cdf probe multtest affy webbioc • 767 views
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@james-w-macdonald-5106
Last seen 2 days ago
United States
Hi Jane, jane janes wrote: > Dear List, > > Recently I installed webbioc on my laptop. It works perfect but our > lab is interested mainly in chicken affymetrix > microarray analysis. (I can use affy and multtest with our chicken > affy CEL files but no further analysis is possible.) No further analysis is possible? Why is that? > I have some perl programming experience and almost no R. Nevertheless > I Installed all the chicken related packages I found on the > bioconductor web site (like chickencdf, chickenprobe, ggahomolgy etc) > and I tried to make webbioc (annaffy) to work with them by modifying > the cgi scripts. > The only output I have been able to acquire was HTML table containing > links to the affymetrix probe description webpages. > I understand that the R packages behind the webbioc interface must be > supplied with the correctly formated microarray data packages to work > properly but > most probably I have been unable to identify the right files in the > bioconductor repository. > Here are and my questions: > Do such affy chicken files (correctly formatted for webbioc) exist? No. > If they do not exist is it possible to be created by using the already > available R modules and packages? Possible, yes. Easy, no. You will need an annotation package to add any more links to your webpage. To do so you will need the AnnBuilder package. Unfortunately, AnnBuilder is only directly applicable to human, mouse and rat so you will have to extend it to do chicken, which is a bit of a stretch for someone new to R. You can more easily use the biomaRt package to annotate your data, but you won't be able to use webbioc to do so. Instead you will have to do things directly from within R. You can make HTML tables that are fairly similar to what you would get with webbioc using biomaRt and the annotate package. There is a vignette in biomaRt that shows how to do such a thing. In addition, there are various functions in affycoretools that will allow you to either take an MArrayLM object from limma (a bit more difficult conceptually than multtest, but useful to learn), or simply take a vector of probeset IDs and a list of statistics and create HTML tables fairly easily. Again, there is a vignette in affycoretools that shows how to do this. Best, Jim > > Please excuse me if my question is not very well structured but I am > relatively new recruit > in the world of R and bioinformatics. > Thank you very much in advance for your answers. > > Vassil > > _______________________________________________ > 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 -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.
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@colin-a-smith-325
Last seen 7.4 years ago
Germany
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Nianhua Li ▴ 870
@nianhua-li-1606
Last seen 8.1 years ago
Hi, Jane, AnnBuilder has been extended for chicken last year, but the annotation coverage was not good: http://thread.gmane.org/gmane.science.biology.informatics.conductor/95 87/focus=9780 I just created a chicken annotation package for R 2.5. All the source data (Affymetrix, Entrez, GO, KEGG) were download on Aug, 2006. So, the source data version is consistent with other annotation data packages on bioc 1.9 and 2.0. You can find it at http://www.bioconductor.org/packages/2.0/data/annotation/html/chicken. html The data coverage is still not very good. We extract gene name (nomenclature name) and cytogenetic map from Entrez Gene. Unfortunately, those information is missing for chicken in the source. Quality control information for chicken Date built: Created: Tue Feb 20 17:28:51 2007 Number of probes: 38535 Probe number missmatch: None Probe missmatch: None Mappings found for probe based rda files: chickenACCNUM found 37846 of 38535 chickenCHRLOC found 6718 of 38535 chickenCHR found 22902 of 38535 chickenENTREZID found 23306 of 38535 chickenENZYME found 184 of 38535 chickenGENENAME found 0 of 38535 chickenGO found 11342 of 38535 chickenMAP found 0 of 38535 chickenPATH found 305 of 38535 chickenPMID found 7647 of 38535 chickenREFSEQ found 23050 of 38535 chickenSUMFUNC found 0 of 38535 chickenSYMBOL found 23302 of 38535 chickenUNIGENE found 13617 of 38535 Mappings found for non-probe based rda files: chickenENZYME2PROBE found 88 chickenGO2ALLPROBES found 3247 chickenGO2PROBE found 1848 chickenORGANISM found 1 chickenPATH2PROBE found 60 chickenPFAM found 18588 chickenPMID2PROBE found 2672 chickenPROSITE found 13449 hope this is helpful nianhua
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