Hi Bill -- On 12/31/2012 11:20 AM, wlangdon [guest] wrote: > > Today I wrote to Rafael Irizarry about this and he suggested I post my message here. > > Some time back I wrote some R code to normalise from > one to several tens of thousand Affymetrix cel files on a > (Linux) PC. > > The advantage is that it does not keep all cel files in memory > all the time and so the usual memory limits which restrict the > number of cel files do not apply. > http://www.cs.ucl.ac.uk/staff/W.Langdon/ftp/gp- code/R/TCBB-2007-11-0161_noCEL.tar > > The R-code also reports spatial defects: > A Survey of Spatial Defects in Homo Sapiens Affymetrix GeneChips, > W. B. Langdon and G. J. G. Upton and R. da Silva Camargo and A. P. > Harrison, IEEE/ACM Transactions on Computational Biology and > Bioinformatics, 7(4) 647-653 oct-dec 2010. PubMed 21030732 > > If we could incorporate this into your bioconductor affy package > that would be great. Thank you for the offer. Usually it is better to introduce code as an independent R package. There are instructions on how to do this available with R RShowDoc("R-exts") and of course a large number of miscellaneous web resources including our won http://bioconductor.org/help/course-materials/2012/Seattle- Oct-2012/ Guidelines for the special expectations place on Bioconductor packages are at http://bioconductor.org/developers/package-guidelines/ Also if this sounds a little overwhelming then one possibility might be to suggest this as a 'mentored project' http://bioconductor.org/developers/mentored-projects/ for which a more experienced Bioconductor contributor would need to be identified as a mentor for you. Martin > > Bill > > Dr. W. B. Langdon, > Department of Computer Science, > University College London > Gower Street, London WC1E 6BT, UK > http://www.cs.ucl.ac.uk/staff/W.Langdon/ > > > -- output of sessionInfo(): > > n/a > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > 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 > -- Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793

Martin helpfully suggested that this might become a 'mentored project' http://bioconductor.org/developers/mentored-projects/ Would anyone with more experience of Bioconductor like to help? Thanks Bill -- output of sessionInfo(): n/a -- Sent via the guest posting facility at bioconductor.org.

Dear Martin, Thank you for your quick and helpful reply. On 1/1/13, Martin Morgan <mtmorgan at="" fhcrc.org=""> wrote: > Hi Bill -- > > On 12/31/2012 11:20 AM, wlangdon [guest] wrote: >> >> Today I wrote to Rafael Irizarry about this and he suggested I post my >> message here. >> >> Some time back I wrote some R code to normalise from >> one to several tens of thousand Affymetrix cel files on a >> (Linux) PC. >> >> The advantage is that it does not keep all cel files in memory >> all the time and so the usual memory limits which restrict the >> number of cel files do not apply. >> http://www.cs.ucl.ac.uk/staff/W.Langdon/ftp/gp- code/R/TCBB-2007-11-0161_noCEL.tar >> >> The R-code also reports spatial defects: >> A Survey of Spatial Defects in Homo Sapiens Affymetrix GeneChips, >> W. B. Langdon and G. J. G. Upton and R. da Silva Camargo and A. P. >> Harrison, IEEE/ACM Transactions on Computational Biology and >> Bioinformatics, 7(4) 647-653 oct-dec 2010. PubMed 21030732 >> >> If we could incorporate this into your bioconductor affy package >> that would be great. > > Thank you for the offer. Usually it is better to introduce code as an > independent R package. There are instructions on how to do this available > with R > > RShowDoc("R-exts") > > and of course a large number of miscellaneous web resources including our > won > > http://bioconductor.org/help/course-materials/2012/Seattle- Oct-2012/ > > Guidelines for the special expectations place on Bioconductor packages are > at > > http://bioconductor.org/developers/package-guidelines/ > > Also if this sounds a little overwhelming then one possibility might be to > suggest this as a 'mentored project' > > http://bioconductor.org/developers/mentored-projects/ > > for which a more experienced Bioconductor contributor would need to be > identified as a mentor for you. I'm afraid I am far from a bioconductor expert. So the 'mentored project' route sounds idea. I have posted a reply to my orginal message asking for a mentor. Thanks again Bill > Martin > >> >> Bill >> >> Dr. W. B. Langdon, >> Department of Computer Science, >> University College London >> Gower Street, London WC1E 6BT, UK >> http://www.cs.ucl.ac.uk/staff/W.Langdon/ >> >> >> -- output of sessionInfo(): >> >> n/a >> >> -- >> Sent via the guest posting facility at bioconductor.org. >> >> _______________________________________________ >> 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 >> > > > -- > Computational Biology / Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N. > PO Box 19024 Seattle, WA 98109 > > Location: Arnold Building M1 B861 > Phone: (206) 667-2793 >