Generating GEO submission files from beadarray summary data
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Kemal Akat ▴ 120
@kemal-akat-4351
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Hi all, It's an older post, but can anyone still provide the code Aliaksei and Mark were talking about? Thank you. Kemal https://stat.ethz.ch/pipermail/bioconductor/2012-October/048439.html
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@aliaksei-holik-4992
Last seen 6.5 years ago
Spain/Barcelona/Centre for Genomic Regu…
Hi Kemal, Mark's code needed some modifications, but I did manage to get it to work. I'll send you both the original code and the one with modifications. I wonder if it's worth making it into a package and what that would involve. All the best, Aliaksei. On 15/11/13 3:48 AM, Kemal Akat wrote: > Hi all, > > It's an older post, but can anyone still provide the code Aliaksei and Mark were talking about? > > Thank you. > > Kemal > > https://stat.ethz.ch/pipermail/bioconductor/2012-October/048439.html >
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Hi Aliaksei, That would be great. Thanks. I think it could be useful and if I recall correctly Mark or one of the other others suggest to include it into the beadarray package. Though, most of the users crave for RNA-seq tools I guess. Best, Kemal On Nov 14, 2013, at 4:39 PM, Aliaksei Holik <salvador at="" bio.bsu.by=""> wrote: > Hi Kemal, > > Mark's code needed some modifications, but I did manage to get it to work. I'll send you both the original code and the one with modifications. > > I wonder if it's worth making it into a package and what that would involve. > > All the best, > > Aliaksei. > > On 15/11/13 3:48 AM, Kemal Akat wrote: >> Hi all, >> >> It's an older post, but can anyone still provide the code Aliaksei and Mark were talking about? >> >> Thank you. >> >> Kemal >> >> https://stat.ethz.ch/pipermail/bioconductor/2012-October/048439.html >>
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I'd be glad to add the function to beadarray. Could you send me the code Aliaksei? Best, Mark On Thu, Nov 14, 2013 at 9:57 PM, Kemal Akat <kakat@mail.rockefeller.edu>wrote: > Hi Aliaksei, > > That would be great. Thanks. > > I think it could be useful and if I recall correctly Mark or one of the > other others suggest to include it into the beadarray package. Though, most > of the users crave for RNA-seq tools I guess. > > Best, > Kemal > > > On Nov 14, 2013, at 4:39 PM, Aliaksei Holik <salvador@bio.bsu.by> > wrote: > > > Hi Kemal, > > > > Mark's code needed some modifications, but I did manage to get it to > work. I'll send you both the original code and the one with modifications. > > > > I wonder if it's worth making it into a package and what that would > involve. > > > > All the best, > > > > Aliaksei. > > > > On 15/11/13 3:48 AM, Kemal Akat wrote: > >> Hi all, > >> > >> It's an older post, but can anyone still provide the code Aliaksei and > Mark were talking about? > >> > >> Thank you. > >> > >> Kemal > >> > >> https://stat.ethz.ch/pipermail/bioconductor/2012-October/048439.html > >> > > [[alternative HTML version deleted]]
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Hi Mark, I certainly could send the code, but I'm not sure it'd be much use. It's a heavily patched version of your code, meddled with to get it to work with my data. Not sure if that's what you'd expect. Aliaksei. On 15/11/2013 19:14, Mark Dunning wrote: > I'd be glad to add the function to beadarray. Could you send me the code > Aliaksei? > > Best, > > Mark > > > On Thu, Nov 14, 2013 at 9:57 PM, Kemal Akat <kakat at="" mail.rockefeller.edu=""> <mailto:kakat at="" mail.rockefeller.edu="">> wrote: > > Hi Aliaksei, > > That would be great. Thanks. > > I think it could be useful and if I recall correctly Mark or one of > the other others suggest to include it into the beadarray package. > Though, most of the users crave for RNA-seq tools I guess. > > Best, > Kemal > > > On Nov 14, 2013, at 4:39 PM, Aliaksei Holik <salvador at="" bio.bsu.by=""> <mailto:salvador at="" bio.bsu.by="">> > wrote: > > > Hi Kemal, > > > > Mark's code needed some modifications, but I did manage to get it > to work. I'll send you both the original code and the one with > modifications. > > > > I wonder if it's worth making it into a package and what that > would involve. > > > > All the best, > > > > Aliaksei. > > > > On 15/11/13 3:48 AM, Kemal Akat wrote: > >> Hi all, > >> > >> It's an older post, but can anyone still provide the code > Aliaksei and Mark were talking about? > >> > >> Thank you. > >> > >> Kemal > >> > >> https://stat.ethz.ch/pipermail/bioconductor/2012-October/048439.html > >> > >
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I just realised that there is already a 'GEOSubmission' package on Bioconductor. Did you already try this package? Perhaps this would be a more-logical place for the conversion script to exist? Mark On Thu, Nov 14, 2013 at 9:57 PM, Kemal Akat <kakat@mail.rockefeller.edu>wrote: > Hi Aliaksei, > > That would be great. Thanks. > > I think it could be useful and if I recall correctly Mark or one of the > other others suggest to include it into the beadarray package. Though, most > of the users crave for RNA-seq tools I guess. > > Best, > Kemal > > > On Nov 14, 2013, at 4:39 PM, Aliaksei Holik <salvador@bio.bsu.by> > wrote: > > > Hi Kemal, > > > > Mark's code needed some modifications, but I did manage to get it to > work. I'll send you both the original code and the one with modifications. > > > > I wonder if it's worth making it into a package and what that would > involve. > > > > All the best, > > > > Aliaksei. > > > > On 15/11/13 3:48 AM, Kemal Akat wrote: > >> Hi all, > >> > >> It's an older post, but can anyone still provide the code Aliaksei and > Mark were talking about? > >> > >> Thank you. > >> > >> Kemal > >> > >> https://stat.ethz.ch/pipermail/bioconductor/2012-October/048439.html > >> > > [[alternative HTML version deleted]]
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Hi, I haven't yet, but the vignette and reference suggest that it works with different platforms. Will try and let you know. Thanks for bringing it to my attention. Kemal On Nov 15, 2013, at 2:50 PM, Mark Dunning <mark.dunning@gmail.com<mailto:mark.dunning@gmail.com>> wrote: I just realised that there is already a 'GEOSubmission' package on Bioconductor. Did you already try this package? Perhaps this would be a more-logical place for the conversion script to exist? Mark On Thu, Nov 14, 2013 at 9:57 PM, Kemal Akat <kakat@mail.rockefeller.edu<mailto:kakat@mail.rockefeller.edu>> wrote: Hi Aliaksei, That would be great. Thanks. I think it could be useful and if I recall correctly Mark or one of the other others suggest to include it into the beadarray package. Though, most of the users crave for RNA-seq tools I guess. Best, Kemal On Nov 14, 2013, at 4:39 PM, Aliaksei Holik <salvador@bio.bsu.by<mailto:salvador@bio.bsu.by>> wrote: > Hi Kemal, > > Mark's code needed some modifications, but I did manage to get it to work. I'll send you both the original code and the one with modifications. > > I wonder if it's worth making it into a package and what that would involve. > > All the best, > > Aliaksei. > > On 15/11/13 3:48 AM, Kemal Akat wrote: >> Hi all, >> >> It's an older post, but can anyone still provide the code Aliaksei and Mark were talking about? >> >> Thank you. >> >> Kemal >> >> https://stat.ethz.ch/pipermail/bioconductor/2012-October/048439.html >> [[alternative HTML version deleted]]
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Hi Mark and Kemal, The reason I needed the code in the first instance is because the GEOsubmission function produceGEOSampleInfoTemplate wouldn't work with a beadarray generated object. This is what I got in response from Tim Triche: On 03/10/2012 15:56, Tim Triche, Jr. wrote: > yes, you need it to be a LumiBatch or other preprocessing-annotated > object in order for the information to be found > > ExpressionSetIllumina apparently doesn't contain that information. > try running traceback() after you get the error Mind, this was more than a year ago and perhaps this functionality has been added. All the best, Aliaksei. On 16/11/2013 06:50, Mark Dunning wrote: > I just realised that there is already a 'GEOSubmission' package on > Bioconductor. Did you already try this package? Perhaps this would be a > more-logical place for the conversion script to exist? > > Mark > > > On Thu, Nov 14, 2013 at 9:57 PM, Kemal Akat <kakat at="" mail.rockefeller.edu=""> <mailto:kakat at="" mail.rockefeller.edu="">> wrote: > > Hi Aliaksei, > > That would be great. Thanks. > > I think it could be useful and if I recall correctly Mark or one of > the other others suggest to include it into the beadarray package. > Though, most of the users crave for RNA-seq tools I guess. > > Best, > Kemal > > > On Nov 14, 2013, at 4:39 PM, Aliaksei Holik <salvador at="" bio.bsu.by=""> <mailto:salvador at="" bio.bsu.by="">> > wrote: > > > Hi Kemal, > > > > Mark's code needed some modifications, but I did manage to get it > to work. I'll send you both the original code and the one with > modifications. > > > > I wonder if it's worth making it into a package and what that > would involve. > > > > All the best, > > > > Aliaksei. > > > > On 15/11/13 3:48 AM, Kemal Akat wrote: > >> Hi all, > >> > >> It's an older post, but can anyone still provide the code > Aliaksei and Mark were talking about? > >> > >> Thank you. > >> > >> Kemal > >> > >> https://stat.ethz.ch/pipermail/bioconductor/2012-October/048439.html > >> > >
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