Question: Looking for R package for Nimblegen expression data
0
gravatar for Xinxia Peng
12.9 years ago by
Xinxia Peng120
Xinxia Peng120 wrote:
I was told by Nimblegen that the XYS file is not always available for expression data. Any suggestions? Thanks, Xinxia -----Original Message----- From: Benilton Carvalho [mailto:bcarvalh@jhsph.edu] Sent: Monday, January 29, 2007 10:00 AM To: Xinxia Peng Cc: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] Looking for R package for Nimblegen expression data Yes, my bad not mentioning that... it's in the devel branch and it does requires R-2.5.0. b On Jan 29, 2007, at 12:58 PM, Xinxia Peng wrote: > Great. Is it the devel package? It seems that it needs R 2.5.0? > > Xinxia > > -----Original Message----- > From: Benilton Carvalho [mailto:bcarvalh at jhsph.edu] > Sent: Monday, January 29, 2007 9:49 AM > To: Xinxia Peng > Cc: bioconductor at stat.math.ethz.ch > Subject: Re: [BioC] Looking for R package for Nimblegen expression > data > > The oligo package handles those, and you'll need to use the > makePlatformDesign package to build the data pkg required for > analysis. > > The following might be helpful: > > http://www.bioconductor.org/workshops/2006/BioC2006/labs/bcarvalho/ > tutorial-slides.pdf > > and contact me if you need any help regarding this, given that the > documentation is not ready. > > b > > On Jan 29, 2007, at 12:18 PM, Xinxia Peng wrote: > >> Hello, >> >> Could someone suggest a R package for handling Nimblegen expression >> arrays? >> >> Thanks, >> Xinxia
oligo makeplatformdesign • 502 views
ADD COMMENTlink modified 12.9 years ago • written 12.9 years ago by Xinxia Peng120
Answer: Looking for R package for Nimblegen expression data
0
gravatar for Xinxia Peng
12.9 years ago by
Xinxia Peng120
Xinxia Peng120 wrote:
Great. I will do that. Thanks, Xinxia -----Original Message----- From: Todd Richmond [mailto:todd@nimblegen.com] Sent: Thursday, February 01, 2007 1:28 PM To: Xinxia Peng Cc: Benilton Carvalho; bioconductor at stat.math.ethz.ch Subject: Re: [BioC] Looking for R package for Nimblegen expression data Hi Xinxia, With apologies to Benilton, XYS files are not yet part of the standard deliverables from our service lab. However, you can request them from Tech Services and they will provide them for any recent order. Regards, Todd Xinxia Peng wrote: > I was told by Nimblegen that the XYS file is not always available for > expression data. Any suggestions? > > Thanks, > Xinxia > > > -----Original Message----- > From: Benilton Carvalho [mailto:bcarvalh at jhsph.edu] > Sent: Monday, January 29, 2007 10:00 AM > To: Xinxia Peng > Cc: bioconductor at stat.math.ethz.ch > Subject: Re: [BioC] Looking for R package for Nimblegen expression > data > > Yes, my bad not mentioning that... it's in the devel branch and it > does requires R-2.5.0. > b > > On Jan 29, 2007, at 12:58 PM, Xinxia Peng wrote: > >> Great. Is it the devel package? It seems that it needs R 2.5.0? >> >> Xinxia >> >> -----Original Message----- >> From: Benilton Carvalho [mailto:bcarvalh at jhsph.edu] >> Sent: Monday, January 29, 2007 9:49 AM >> To: Xinxia Peng >> Cc: bioconductor at stat.math.ethz.ch >> Subject: Re: [BioC] Looking for R package for Nimblegen expression >> data >> >> The oligo package handles those, and you'll need to use the >> makePlatformDesign package to build the data pkg required for >> analysis. >> >> The following might be helpful: >> >> http://www.bioconductor.org/workshops/2006/BioC2006/labs/bcarvalho/ >> tutorial-slides.pdf >> >> and contact me if you need any help regarding this, given that the >> documentation is not ready. >> >> b >> >> On Jan 29, 2007, at 12:18 PM, Xinxia Peng wrote: >> >>> Hello, >>> >>> Could someone suggest a R package for handling Nimblegen expression >>> arrays? >>> >>> Thanks, >>> Xinxia > > _______________________________________________ > 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 > > -- Todd Richmond, PhD Manager of Research Informatics NimbleGen Systems, Inc Madison, WI 53719 1-608-218-7600
ADD COMMENTlink written 12.9 years ago by Xinxia Peng120
Answer: Looking for R package for Nimblegen expression data
0
gravatar for Todd Richmond
12.9 years ago by
Todd Richmond140
Todd Richmond140 wrote:
Hi Xinxia, With apologies to Benilton, XYS files are not yet part of the standard deliverables from our service lab. However, you can request them from Tech Services and they will provide them for any recent order. Regards, Todd Xinxia Peng wrote: > I was told by Nimblegen that the XYS file is not always available for > expression data. Any suggestions? > > Thanks, > Xinxia > > > -----Original Message----- > From: Benilton Carvalho [mailto:bcarvalh at jhsph.edu] > Sent: Monday, January 29, 2007 10:00 AM > To: Xinxia Peng > Cc: bioconductor at stat.math.ethz.ch > Subject: Re: [BioC] Looking for R package for Nimblegen expression data > > Yes, my bad not mentioning that... it's in the devel branch and it does > requires R-2.5.0. > b > > On Jan 29, 2007, at 12:58 PM, Xinxia Peng wrote: > >> Great. Is it the devel package? It seems that it needs R 2.5.0? >> >> Xinxia >> >> -----Original Message----- >> From: Benilton Carvalho [mailto:bcarvalh at jhsph.edu] >> Sent: Monday, January 29, 2007 9:49 AM >> To: Xinxia Peng >> Cc: bioconductor at stat.math.ethz.ch >> Subject: Re: [BioC] Looking for R package for Nimblegen expression >> data >> >> The oligo package handles those, and you'll need to use the >> makePlatformDesign package to build the data pkg required for >> analysis. >> >> The following might be helpful: >> >> http://www.bioconductor.org/workshops/2006/BioC2006/labs/bcarvalho/ >> tutorial-slides.pdf >> >> and contact me if you need any help regarding this, given that the >> documentation is not ready. >> >> b >> >> On Jan 29, 2007, at 12:18 PM, Xinxia Peng wrote: >> >>> Hello, >>> >>> Could someone suggest a R package for handling Nimblegen expression >>> arrays? >>> >>> Thanks, >>> Xinxia > > _______________________________________________ > 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 > > -- Todd Richmond, PhD Manager of Research Informatics NimbleGen Systems, Inc Madison, WI 53719 1-608-218-7600
ADD COMMENTlink written 12.9 years ago by Todd Richmond140
Hi Todd, it's good to see a reply from Nimblegen here. I tried repeatedly to get info from Tech Services regarding our arrays and I got absolute silence for response. A colleague of mine had a similar experience, but she kept insisting and eventually she was given the email of Michael Hogan, who was very good, it must be said. Commenting these issues with other people in Holland I found I wasn't the only one feeling Nimblegen's support is "patchy". Eventually you can get through to somebody who will be helpful, but you have to insist. So, my question is... can you suggest what's the best way to contact Nimblegen (either Support or Tech Services) and get an answer? Emailing through the forms on the website led me nowhere in the past. regards, Jose Quoting Todd Richmond <todd at="" nimblegen.com="">: > Hi Xinxia, > > With apologies to Benilton, XYS files are not yet part of the standard > deliverables from our service lab. However, you can request them from > Tech Services and they will provide them for any recent order. > > Regards, > Todd > > Xinxia Peng wrote: >> I was told by Nimblegen that the XYS file is not always available for >> expression data. Any suggestions? >> >> Thanks, >> Xinxia >> >> >> -----Original Message----- >> From: Benilton Carvalho [mailto:bcarvalh at jhsph.edu] >> Sent: Monday, January 29, 2007 10:00 AM >> To: Xinxia Peng >> Cc: bioconductor at stat.math.ethz.ch >> Subject: Re: [BioC] Looking for R package for Nimblegen expression data >> >> Yes, my bad not mentioning that... it's in the devel branch and it does >> requires R-2.5.0. >> b >> >> On Jan 29, 2007, at 12:58 PM, Xinxia Peng wrote: >> >>> Great. Is it the devel package? It seems that it needs R 2.5.0? >>> >>> Xinxia >>> >>> -----Original Message----- >>> From: Benilton Carvalho [mailto:bcarvalh at jhsph.edu] >>> Sent: Monday, January 29, 2007 9:49 AM >>> To: Xinxia Peng >>> Cc: bioconductor at stat.math.ethz.ch >>> Subject: Re: [BioC] Looking for R package for Nimblegen expression >>> data >>> >>> The oligo package handles those, and you'll need to use the >>> makePlatformDesign package to build the data pkg required for >>> analysis. >>> >>> The following might be helpful: >>> >>> http://www.bioconductor.org/workshops/2006/BioC2006/labs/bcarvalho/ >>> tutorial-slides.pdf >>> >>> and contact me if you need any help regarding this, given that the >>> documentation is not ready. >>> >>> b >>> >>> On Jan 29, 2007, at 12:18 PM, Xinxia Peng wrote: >>> >>>> Hello, >>>> >>>> Could someone suggest a R package for handling Nimblegen expression >>>> arrays? >>>> >>>> Thanks, >>>> Xinxia >> >> _______________________________________________ >> 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 >> >> > > > -- > Todd Richmond, PhD > Manager of Research Informatics > NimbleGen Systems, Inc > Madison, WI 53719 > 1-608-218-7600 > > _______________________________________________ > 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 > > -- Dr. Jose I. de las Heras Email: J.delasHeras at ed.ac.uk The Wellcome Trust Centre for Cell Biology Phone: +44 (0)131 6513374 Institute for Cell & Molecular Biology Fax: +44 (0)131 6507360 Swann Building, Mayfield Road University of Edinburgh Edinburgh EH9 3JR UK
ADD REPLYlink written 12.9 years ago by J.delasHeras@ed.ac.uk1.9k
Hi Jose, I'm sorry to hear that you've had problems getting help from our Technical Services group. I read the BioConductor list and I'm happy to answer what questions I can, especially with regard to BioConductor issues. The best way to get help is to directly email techsupport at nimblegen.com with your questions, or to call them at 1 (877) NimbleGen. I can tell you that they are a hard-working group of people (all 3 of them!) who have to answer questions ranging from array design, sample preparation, hybridization all the way through to data analysis, as well as handling training and a lot of documentation. And when they have difficult questions they have to pry the answers out of equally busy bioinformatics poeple. So hopefully you'll forgive them if they are sometimes slow to respond, or can't answer your questions right away. Thanks, Todd On 7:21:36 02/02/07 J.delasHeras at ed.ac.uk wrote: > Hi Todd, > > it's good to see a reply from Nimblegen here. > > I tried repeatedly to get info from Tech Services regarding our > arrays and I got absolute silence for response. > A colleague of mine had a similar experience, but she kept insisting > and eventually she was given the email of Michael Hogan, who was very > good, it must be said. > Commenting these issues with other people in Holland I found I wasn't > the only one feeling Nimblegen's support is "patchy". Eventually you > can get through to somebody who will be helpful, but you have to > insist. > So, my question is... can you suggest what's the best way to contact > Nimblegen (either Support or Tech Services) and get an answer? > Emailing through the forms on the website led me nowhere in the past. > > regards, > > Jose > > > > Quoting Todd Richmond <todd at="" nimblegen.com="">: > > > Hi Xinxia, > > > > With apologies to Benilton, XYS files are not yet part of the > > standard deliverables from our service lab. However, you can > > request them from Tech Services and they will provide them for any > > recent order. > > Regards, > > Todd > > > > Xinxia Peng wrote: > >> I was told by Nimblegen that the XYS file is not always available > >> for expression data. Any suggestions? > >> > >> Thanks, > >> Xinxia > >> > >> > >> -----Original Message----- > >> From: Benilton Carvalho [mailto:bcarvalh at jhsph.edu] > >> Sent: Monday, January 29, 2007 10:00 AM > >> To: Xinxia Peng > >> Cc: bioconductor at stat.math.ethz.ch > >> Subject: Re: [BioC] Looking for R package for Nimblegen > >> expression data > >> Yes, my bad not mentioning that... it's in the devel branch and > >> it does requires R-2.5.0. > >> b > >> > >> On Jan 29, 2007, at 12:58 PM, Xinxia Peng wrote: > >> > >>> Great. Is it the devel package? It seems that it needs R 2.5.0? > >>> > >>> Xinxia > >>> > >>> -----Original Message----- > >>> From: Benilton Carvalho [mailto:bcarvalh at jhsph.edu] > >>> Sent: Monday, January 29, 2007 9:49 AM > >>> To: Xinxia Peng > >>> Cc: bioconductor at stat.math.ethz.ch > >>> Subject: Re: [BioC] Looking for R package for Nimblegen > >>> expression data > >>> > >>> The oligo package handles those, and you'll need to use the > >>> makePlatformDesign package to build the data pkg required for > >>> analysis. > >>> > >>> The following might be helpful: > >>> > >>> http://www.bioconductor.org/workshops/2006/BioC2006/labs/bcarvalh > >>> o/ > >>> tutorial-slides.pdf > >>> > >>> and contact me if you need any help regarding this, given that > >>> the documentation is not ready. > >>> > >>> b > >>> > >>> On Jan 29, 2007, at 12:18 PM, Xinxia Peng wrote: > >>> > >>>> Hello, > >>>> > >>>> Could someone suggest a R package for handling Nimblegen > >>>> expression arrays? > >>>> > >>>> Thanks, > >>>> Xinxia > >> > >> _______________________________________________ > >> 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 > >> > >> > > > > > > -- > > Todd Richmond, PhD > > Manager of Research Informatics > > NimbleGen Systems, Inc > > Madison, WI 53719 > > 1-608-218-7600 > > > > _______________________________________________ > > 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 > > > > > > > > -- > Dr. Jose I. de las Heras Email: > J.delasHeras at ed.ac.uk The Wellcome Trust Centre for Cell Biology > Phone: +44 (0)131 6513374 Institute for Cell & Molecular Biology > Fax: +44 (0)131 6507360 Swann Building, Mayfield Road > University of Edinburgh > Edinburgh EH9 3JR > UK >
ADD REPLYlink written 12.9 years ago by Todd Richmond140
Jose, Todd forwarded this message onto Technical Support. In technical support we try our best to address all of the emails, phone calls, and voicemail messages that we get within 24 hours. I searched the Tech Support Inbox and check the all of our voicemail boxes, including the phone of the person that is out of the office this week, and I did not find any message from Dr. De Las Heras from the University of Edinburgh. However, I have been in contact with Xinxia from Seattle Biomedical Research Institute a number of times with week via both email and phone. Please let me know if there is anything that I can help you with. Thank You, Marie Uphoff NimbleGen Technical Support -----Original Message----- From: Todd Richmond [mailto:todd@nimblegen.com] Sent: Friday, February 02, 2007 9:07 AM To: J.delasHeras at ed.ac.uk Cc: xinxia.peng at sbri.org; bioconductor at stat.math.ethz.ch; todd at nimblegen.com; techsupport at nimblegen.com Subject: Re: [BioC] Looking for R package for Nimblegen expression data Hi Jose, I'm sorry to hear that you've had problems getting help from our Technical Services group. I read the BioConductor list and I'm happy to answer what questions I can, especially with regard to BioConductor issues. The best way to get help is to directly email techsupport at nimblegen.com with your questions, or to call them at 1 (877) NimbleGen. I can tell you that they are a hard-working group of people (all 3 of them!) who have to answer questions ranging from array design, sample preparation, hybridization all the way through to data analysis, as well as handling training and a lot of documentation. And when they have difficult questions they have to pry the answers out of equally busy bioinformatics poeple. So hopefully you'll forgive them if they are sometimes slow to respond, or can't answer your questions right away. Thanks, Todd On 7:21:36 02/02/07 J.delasHeras at ed.ac.uk wrote: > Hi Todd, > > it's good to see a reply from Nimblegen here. > > I tried repeatedly to get info from Tech Services regarding our > arrays and I got absolute silence for response. > A colleague of mine had a similar experience, but she kept insisting > and eventually she was given the email of Michael Hogan, who was very > good, it must be said. > Commenting these issues with other people in Holland I found I wasn't > the only one feeling Nimblegen's support is "patchy". Eventually you > can get through to somebody who will be helpful, but you have to > insist. > So, my question is... can you suggest what's the best way to contact > Nimblegen (either Support or Tech Services) and get an answer? > Emailing through the forms on the website led me nowhere in the past. > > regards, > > Jose > > > > Quoting Todd Richmond <todd at="" nimblegen.com="">: > > > Hi Xinxia, > > > > With apologies to Benilton, XYS files are not yet part of the > > standard deliverables from our service lab. However, you can > > request them from Tech Services and they will provide them for any > > recent order. > > Regards, > > Todd > > > > Xinxia Peng wrote: > >> I was told by Nimblegen that the XYS file is not always available > >> for expression data. Any suggestions? > >> > >> Thanks, > >> Xinxia > >> > >> > >> -----Original Message----- > >> From: Benilton Carvalho [mailto:bcarvalh at jhsph.edu] > >> Sent: Monday, January 29, 2007 10:00 AM > >> To: Xinxia Peng > >> Cc: bioconductor at stat.math.ethz.ch > >> Subject: Re: [BioC] Looking for R package for Nimblegen > >> expression data > >> Yes, my bad not mentioning that... it's in the devel branch and > >> it does requires R-2.5.0. > >> b > >> > >> On Jan 29, 2007, at 12:58 PM, Xinxia Peng wrote: > >> > >>> Great. Is it the devel package? It seems that it needs R 2.5.0? > >>> > >>> Xinxia > >>> > >>> -----Original Message----- > >>> From: Benilton Carvalho [mailto:bcarvalh at jhsph.edu] > >>> Sent: Monday, January 29, 2007 9:49 AM > >>> To: Xinxia Peng > >>> Cc: bioconductor at stat.math.ethz.ch > >>> Subject: Re: [BioC] Looking for R package for Nimblegen > >>> expression data > >>> > >>> The oligo package handles those, and you'll need to use the > >>> makePlatformDesign package to build the data pkg required for > >>> analysis. > >>> > >>> The following might be helpful: > >>> > >>> http://www.bioconductor.org/workshops/2006/BioC2006/labs/bcarvalh > >>> o/ > >>> tutorial-slides.pdf > >>> > >>> and contact me if you need any help regarding this, given that > >>> the documentation is not ready. > >>> > >>> b > >>> > >>> On Jan 29, 2007, at 12:18 PM, Xinxia Peng wrote: > >>> > >>>> Hello, > >>>> > >>>> Could someone suggest a R package for handling Nimblegen > >>>> expression arrays? > >>>> > >>>> Thanks, > >>>> Xinxia > >> > >> _______________________________________________ > >> 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 > >> > >> > > > > > > -- > > Todd Richmond, PhD > > Manager of Research Informatics > > NimbleGen Systems, Inc > > Madison, WI 53719 > > 1-608-218-7600 > > > > _______________________________________________ > > 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 > > > > > > > > -- > Dr. Jose I. de las Heras Email: > J.delasHeras at ed.ac.uk The Wellcome Trust Centre for Cell Biology > Phone: +44 (0)131 6513374 Institute for Cell & Molecular Biology > Fax: +44 (0)131 6507360 Swann Building, Mayfield Road > University of Edinburgh > Edinburgh EH9 3JR > UK >
ADD REPLYlink written 12.9 years ago by Tech Support10
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