Problem with "ragene10stprobeset.db" package
2
0
Entering edit mode
@laura-bermudez-5107
Last seen 9.6 years ago
Dear Bioconductor Team: I am using the Bioconductor annotation package "ragene10stprobeset.db" for an analysis of differential expression, but when I want to annotate my Arrays selection ("10700001" "10700005" "10700013" "10700063" ... etc..), it shows me “value for "10700063" not found”. Why can this happen? Thanks for your help. Laura [[alternative HTML version deleted]]
Annotation annotate Annotation annotate • 1.5k views
ADD COMMENT
0
Entering edit mode
@james-w-macdonald-5106
Last seen 4 hours ago
United States
Hi Laura, On 5/3/2012 7:03 AM, Laura Berm?dez wrote: > Dear Bioconductor Team: > > > > I am using the Bioconductor annotation package "ragene10stprobeset.db" for > an analysis of differential expression, but when I want to annotate my > Arrays selection ("10700001" "10700005" "10700013" "10700063" ... etc..), it > shows me ?value for "10700063" not found?. Why can this happen? You don't give us much to go on. In future, please give us some code and the results from running sessionInfo() at an R prompt. If I break out my crystal ball, I can divine that you have done something like library(oligo) abatch <- read.celfiles(celfiles) eset <- rma(abatch) or library(affy) abatch <- ReadAffy() eset <- rma(abatch) In either case, what you have done is summarize data at the _transcript_ level. Note here that using oligo, you can also summarize at the probeset level, which is pretty close to summarizing by exon. Since my crystal ball tells me you summarized at the transcript level, you will also need to annotate at the transcript level. In which case you need the ragene10sttranscriptcluster.db package. Best, Jim > > > > Thanks for your help. > > > > Laura > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > 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 -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099
ADD COMMENT
0
Entering edit mode
Ekta Jain ▴ 370
@ekta-jain-5131
Last seen 9.6 years ago
Dear All, The lumiHumanIDMapping package does not seem to have the windows binary files available on the Bioconductor website - http://www.biocon ductor.org/packages/release/data/annotation/html/lumiHumanIDMapping.ht ml Can anyone please tell me where i can get the same .gz package from? Many Thanks, Ekta Senior Research Associate Bioinformatics Department Jubilant Biosys Pvt Ltd, #96, Industrial Suburb, 2nd Stage Yeshwantpur, Bangalore 560 022 Ph No : +91-80-66628346 The information contained in this electronic message and in any attachments to this message is confidential, legally privileged and intended only for use by the person or entity to which this electronic message is addressed. If you are not the intended recipient, and have received this message in error, please notify the sender and system manager by return email and delete the message and its attachments and also you are hereby notified that any distribution, copying, review, retransmission, dissemination or other use of this electronic transmission or the information contained in it is strictly prohibited. Please note that any views or opinions presented in this email are solely those of the author and may not represent those of the Company or bind the Company. Any commitments made over e-mail are not financially binding on the company unless accompanied or followed by a valid purchase order. This message has been scanned for viruses and dangerous content by Mail Scanner, and is believed to be clean. The Company accepts no liability for any damage caused by any virus transmitted by this email. www.jubl.com
ADD COMMENT
0
Entering edit mode
On Thu, May 3, 2012 at 4:39 AM, Ekta Jain <ekta_jain at="" jubilantbiosys.com=""> wrote: > Dear All, > The lumiHumanIDMapping package does not seem to have the windows binary files available on the Bioconductor website - http://www.biocon ductor.org/packages/release/data/annotation/html/lumiHumanIDMapping.ht ml > > Can anyone please tell me where i can get the same .gz package from? I'll look into why this is not available for windows, but in the meantime you can install it as follows: source("http://bioconductor.org/biocLite.R") biocLite("lumiHumanIDMapping", type="source") Dan > > Many Thanks, > Ekta > Senior Research Associate > Bioinformatics Department > Jubilant Biosys Pvt Ltd, > #96, Industrial Suburb, 2nd Stage > Yeshwantpur, Bangalore 560 022 > Ph No : +91-80-66628346 > > > The information contained in this electronic message and in any attachments to this message is confidential, legally privileged and intended only for use by the person or entity to which this electronic message is addressed. If you are not the intended recipient, and have received this message in error, please notify the sender and system manager by return email and delete the message and its attachments and also you are hereby notified that any distribution, copying, review, retransmission, dissemination or other use of this electronic transmission or the information contained in it is strictly prohibited. Please note that any views or opinions presented in this email are solely those of the author and may not represent those of the Company or bind the Company. Any commitments made over e-mail are not financially binding on the company unless accompanied or followed by a valid purchase order. This message has been scanned for viruses and dangerous content by Mail Scanner, a! > ?nd is believed to be clean. The Company accepts no liability for any damage caused by any virus transmitted by this email. > www.jubl.com > > _______________________________________________ > 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
ADD REPLY
0
Entering edit mode
Dear Dan, That wouldn't work as well. If we don't have the package available on Bioconductor.org then biocLite will not be able to download it. I did originally start with the way you suggested. When it didn't work thought of downloading the relevant .gz file from Bioconductor, which is not available. Any help would be great !!! Thanks, Ekta -----Original Message----- From: Dan Tenenbaum [mailto:dtenenba@fhcrc.org] Sent: 03 May 2012 23:22 To: Ekta Jain Cc: bioconductor at r-project.org Subject: Re: [BioC] lumiHumanIDMapping package does not exist for windows? On Thu, May 3, 2012 at 4:39 AM, Ekta Jain <ekta_jain at="" jubilantbiosys.com=""> wrote: > Dear All, > The lumiHumanIDMapping package does not seem to have the windows binary files available on the Bioconductor website - http://www.biocon ductor.org/packages/release/data/annotation/html/lumiHumanIDMapping.ht ml > > Can anyone please tell me where i can get the same .gz package from? I'll look into why this is not available for windows, but in the meantime you can install it as follows: source("http://bioconductor.org/biocLite.R") biocLite("lumiHumanIDMapping", type="source") Dan > > Many Thanks, > Ekta > Senior Research Associate > Bioinformatics Department > Jubilant Biosys Pvt Ltd, > #96, Industrial Suburb, 2nd Stage > Yeshwantpur, Bangalore 560 022 > Ph No : +91-80-66628346 > > > The information contained in this electronic message and in any attachments to this message is confidential, legally privileged and intended only for use by the person or entity to which this electronic message is addressed. If you are not the intended recipient, and have received this message in error, please notify the sender and system manager by return email and delete the message and its attachments and also you are hereby notified that any distribution, copying, review, retransmission, dissemination or other use of this electronic transmission or the information contained in it is strictly prohibited. Please note that any views or opinions presented in this email are solely those of the author and may not represent those of the Company or bind the Company. Any commitments made over e-mail are not financially binding on the company unless accompanied or followed by a valid purchase order. This message has been scanned for viruses and dangerous content by Mail Scanner, a! > ?nd is believed to be clean. The Company accepts no liability for any damage caused by any virus transmitted by this email. > www.jubl.com > > _______________________________________________ > 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 The information contained in this electronic message and in any attachments to this message is confidential, legally privileged and intended only for use by the person or entity to which this electronic message is addressed. If you are not the intended recipient, and have received this message in error, please notify the sender and system manager by return email and delete the message and its attachments and also you are hereby notified that any distribution, copying, review, retransmission, dissemination or other use of this electronic transmission or the information contained in it is strictly prohibited. Please note that any views or opinions presented in this email are solely those of the author and may not represent those of the Company or bind the Company. Any commitments made over e-mail are not financially binding on the company unless accompanied or followed by a valid purchase order. This message has been scanned for viruses and dangerous content by Mail Scanner, and is believed to be clean. The Company accepts no liability for any damage caused by any virus transmitted by this email. www.jubl.com
ADD REPLY
0
Entering edit mode
On Thu, May 3, 2012 at 8:35 PM, Ekta Jain <ekta_jain at="" jubilantbiosys.com=""> wrote: > Dear Dan, > That wouldn't work as well. If we don't have the package available on Bioconductor.org then biocLite will not be able to download it. > What is the exact error message, and the output of sessionInfo()? Also what is the output of getOption("BioC_mirror") ? > I did originally start with the way you suggested. When it didn't work thought of downloading the relevant .gz file from Bioconductor, which is not available. > The .gz file is available, see the you emailed. However, biocLite() is the preferred way to install it, so let's figure out why that is not working. Dan > Any help would be great !!! > > Thanks, > Ekta > > -----Original Message----- > From: Dan Tenenbaum [mailto:dtenenba at fhcrc.org] > Sent: 03 May 2012 23:22 > To: Ekta Jain > Cc: bioconductor at r-project.org > Subject: Re: [BioC] lumiHumanIDMapping package does not exist for windows? > > On Thu, May 3, 2012 at 4:39 AM, Ekta Jain <ekta_jain at="" jubilantbiosys.com=""> wrote: >> Dear All, >> The lumiHumanIDMapping package does not seem to have the windows binary files available on the Bioconductor website - http://www.biocon ductor.org/packages/release/data/annotation/html/lumiHumanIDMapping.ht ml >> >> Can anyone please tell me where i can get the same .gz package from? > > I'll look into why this is not available for windows, but in the > meantime you can install it as follows: > > source("http://bioconductor.org/biocLite.R") > biocLite("lumiHumanIDMapping", type="source") > > Dan > >> >> Many Thanks, >> Ekta >> Senior Research Associate >> Bioinformatics Department >> Jubilant Biosys Pvt Ltd, >> #96, Industrial Suburb, 2nd Stage >> Yeshwantpur, Bangalore 560 022 >> Ph No : +91-80-66628346 >> >> >> The information contained in this electronic message and in any attachments to this message is confidential, legally privileged and intended only for use by the person or entity to which this electronic message is addressed. If you are not the intended recipient, and have received this message in error, please notify the sender and system manager by return email and delete the message and its attachments and also you are hereby notified that any distribution, copying, review, retransmission, dissemination or other use of this electronic transmission or the information contained in it is strictly prohibited. Please note that any views or opinions presented in this email are solely those of the author and may not represent those of the Company or bind the Company. Any commitments made over e-mail are not financially binding on the company unless accompanied or followed by a valid purchase order. This message has been scanned for viruses and dangerous content by Mail Scanner, a! >> ?nd is believed to be clean. The Company accepts no liability for any damage caused by any virus transmitted by this email. >> www.jubl.com >> >> _______________________________________________ >> 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 > The information contained in this electronic message and in any attachments to this message is confidential, legally privileged and intended only for use by the person or entity to which this electronic message is addressed. If you are not the intended recipient, and have received this message in error, please notify the sender and system manager by return email and delete the message and its attachments and also you are hereby notified that any distribution, copying, review, retransmission, dissemination or other use of this electronic transmission or the information contained in it is strictly prohibited. Please note that any views or opinions presented in this email are solely those of the author and may not represent those of the Company or bind the Company. Any commitments made over e-mail are not financially binding on the company unless accompanied or followed by a valid purchase order. This message has been scanned for viruses and dangerous content by Mail Scanner, and is believed to be clean. The Company accepts no liability for any damage caused by any virus transmitted by this email. > www.jubl.com >
ADD REPLY
0
Entering edit mode
Dear Dan, Only the tar.gz file is available, the windows binary is not there. Please find below the error messages and sessionInfo. Thanks for your help. Error Message: > source("http://bioconductor.org/biocLite.R") BiocInstaller version 1.4.4, ?biocLite for help > biocLite("lumiHumanIDMapping", type="source") BioC_mirror: http://bioconductor.org Using R version 2.15, BiocInstaller version 1.4.4. Installing package(s) 'lumiHumanIDMapping' trying URL 'http://www.bioconductor.org/packages/2.10/data/annotation/ src/contrib/lumiHumanIDMapping_1.10.0.tar.gz' Error in download.file(url, destfile, method, mode = "wb", ...) : cannot open URL 'http://www.bioconductor.org/packages/2.10/data/anno tation/src/contrib/lumiHumanIDMapping_1.10.0.tar.gz' In addition: Warning message: In download.file(url, destfile, method, mode = "wb", ...) : cannot open: HTTP status was '0 (nil)' Warning in download.packages(pkgs, destdir = tmpd, available = available, : download of package 'lumiHumanIDMapping' failed Old packages: 'GenomicRanges', 'hugene10stv1cdf', 'illuminaHumanv4.db', 'mogene10stv1cdf', 'mogene10stv1probe', 'mouse.db0', 'VariantAnnotation' Update all/some/none? [a/s/n]:a ............... ## From here on the dependencies org.Hs.eg.db do not get installed as well. Error message is given below: Error in read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type")) : cannot open the connection In addition: Warning messages: 1: In unzip(zipname, exdir = dest) : error 1 in extracting from zip file 2: In read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type")) : cannot open compressed file 'org.Hs.eg.db/DESCRIPTION', probable reason 'No such file or directory' > sessionInfo() R version 2.15.0 (2012-03-30) Platform: i386-pc-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=English_India.1252 LC_CTYPE=English_India.1252 [3] LC_MONETARY=English_India.1252 LC_NUMERIC=C [5] LC_TIME=English_India.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] tools_2.15.0 -----Original Message----- From: Dan Tenenbaum [mailto:dtenenba@fhcrc.org] Sent: 04 May 2012 09:25 To: Ekta Jain Cc: bioconductor at r-project.org Subject: Re: [BioC] lumiHumanIDMapping package does not exist for windows? On Thu, May 3, 2012 at 8:35 PM, Ekta Jain <ekta_jain at="" jubilantbiosys.com=""> wrote: > Dear Dan, > That wouldn't work as well. If we don't have the package available on Bioconductor.org then biocLite will not be able to download it. > What is the exact error message, and the output of sessionInfo()? Also what is the output of getOption("BioC_mirror") ? > I did originally start with the way you suggested. When it didn't work thought of downloading the relevant .gz file from Bioconductor, which is not available. > The .gz file is available, see the you emailed. However, biocLite() is the preferred way to install it, so let's figure out why that is not working. Dan > Any help would be great !!! > > Thanks, > Ekta > > -----Original Message----- > From: Dan Tenenbaum [mailto:dtenenba at fhcrc.org] > Sent: 03 May 2012 23:22 > To: Ekta Jain > Cc: bioconductor at r-project.org > Subject: Re: [BioC] lumiHumanIDMapping package does not exist for windows? > > On Thu, May 3, 2012 at 4:39 AM, Ekta Jain <ekta_jain at="" jubilantbiosys.com=""> wrote: >> Dear All, >> The lumiHumanIDMapping package does not seem to have the windows binary files available on the Bioconductor website - http://www.biocon ductor.org/packages/release/data/annotation/html/lumiHumanIDMapping.ht ml >> >> Can anyone please tell me where i can get the same .gz package from? > > I'll look into why this is not available for windows, but in the > meantime you can install it as follows: > > source("http://bioconductor.org/biocLite.R") > biocLite("lumiHumanIDMapping", type="source") > > Dan > >> >> Many Thanks, >> Ekta >> Senior Research Associate >> Bioinformatics Department >> Jubilant Biosys Pvt Ltd, >> #96, Industrial Suburb, 2nd Stage >> Yeshwantpur, Bangalore 560 022 >> Ph No : +91-80-66628346 >> >> >> The information contained in this electronic message and in any attachments to this message is confidential, legally privileged and intended only for use by the person or entity to which this electronic message is addressed. If you are not the intended recipient, and have received this message in error, please notify the sender and system manager by return email and delete the message and its attachments and also you are hereby notified that any distribution, copying, review, retransmission, dissemination or other use of this electronic transmission or the information contained in it is strictly prohibited. Please note that any views or opinions presented in this email are solely those of the author and may not represent those of the Company or bind the Company. Any commitments made over e-mail are not financially binding on the company unless accompanied or followed by a valid purchase order. This message has been scanned for viruses and dangerous content by Mail Scanner, a! >> ?nd is believed to be clean. The Company accepts no liability for any damage caused by any virus transmitted by this email. >> www.jubl.com >> >> _______________________________________________ >> 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 > The information contained in this electronic message and in any attachments to this message is confidential, legally privileged and intended only for use by the person or entity to which this electronic message is addressed. If you are not the intended recipient, and have received this message in error, please notify the sender and system manager by return email and delete the message and its attachments and also you are hereby notified that any distribution, copying, review, retransmission, dissemination or other use of this electronic transmission or the information contained in it is strictly prohibited. Please note that any views or opinions presented in this email are solely those of the author and may not represent those of the Company or bind the Company. Any commitments made over e-mail are not financially binding on the company unless accompanied or followed by a valid purchase order. This message has been scanned for viruses and dangerous content by Mail Scanner, and is believed to be clean. The Company accepts no liability for any damage caused by any virus transmitted by this email. > www.jubl.com > The information contained in this electronic message and in any attachments to this message is confidential, legally privileged and intended only for use by the person or entity to which this electronic message is addressed. If you are not the intended recipient, and have received this message in error, please notify the sender and system manager by return email and delete the message and its attachments and also you are hereby notified that any distribution, copying, review, retransmission, dissemination or other use of this electronic transmission or the information contained in it is strictly prohibited. Please note that any views or opinions presented in this email are solely those of the author and may not represent those of the Company or bind the Company. Any commitments made over e-mail are not financially binding on the company unless accompanied or followed by a valid purchase order. This message has been scanned for viruses and dangerous content by Mail Scanner, and is believed to be clean. The Company accepts no liability for any damage caused by any virus transmitted by this email. www.jubl.com
ADD REPLY
0
Entering edit mode
Hi Dan, Found the windows package at http://bioc.ism.ac.jp/2.8/data/annotation/html/lumiHumanIDMapping.html I am going to download and use this as a locally downloaded package. It is version 1.10 which I think is the latest version? Regards, Ekta -----Original Message----- From: Dan Tenenbaum [mailto:dtenenba@fhcrc.org] Sent: 04 May 2012 09:25 To: Ekta Jain Cc: bioconductor at r-project.org Subject: Re: [BioC] lumiHumanIDMapping package does not exist for windows? On Thu, May 3, 2012 at 8:35 PM, Ekta Jain <ekta_jain at="" jubilantbiosys.com=""> wrote: > Dear Dan, > That wouldn't work as well. If we don't have the package available on Bioconductor.org then biocLite will not be able to download it. > What is the exact error message, and the output of sessionInfo()? Also what is the output of getOption("BioC_mirror") ? > I did originally start with the way you suggested. When it didn't work thought of downloading the relevant .gz file from Bioconductor, which is not available. > The .gz file is available, see the you emailed. However, biocLite() is the preferred way to install it, so let's figure out why that is not working. Dan > Any help would be great !!! > > Thanks, > Ekta > > -----Original Message----- > From: Dan Tenenbaum [mailto:dtenenba at fhcrc.org] > Sent: 03 May 2012 23:22 > To: Ekta Jain > Cc: bioconductor at r-project.org > Subject: Re: [BioC] lumiHumanIDMapping package does not exist for windows? > > On Thu, May 3, 2012 at 4:39 AM, Ekta Jain <ekta_jain at="" jubilantbiosys.com=""> wrote: >> Dear All, >> The lumiHumanIDMapping package does not seem to have the windows binary files available on the Bioconductor website - http://www.biocon ductor.org/packages/release/data/annotation/html/lumiHumanIDMapping.ht ml >> >> Can anyone please tell me where i can get the same .gz package from? > > I'll look into why this is not available for windows, but in the > meantime you can install it as follows: > > source("http://bioconductor.org/biocLite.R") > biocLite("lumiHumanIDMapping", type="source") > > Dan > >> >> Many Thanks, >> Ekta >> Senior Research Associate >> Bioinformatics Department >> Jubilant Biosys Pvt Ltd, >> #96, Industrial Suburb, 2nd Stage >> Yeshwantpur, Bangalore 560 022 >> Ph No : +91-80-66628346 >> >> >> The information contained in this electronic message and in any attachments to this message is confidential, legally privileged and intended only for use by the person or entity to which this electronic message is addressed. If you are not the intended recipient, and have received this message in error, please notify the sender and system manager by return email and delete the message and its attachments and also you are hereby notified that any distribution, copying, review, retransmission, dissemination or other use of this electronic transmission or the information contained in it is strictly prohibited. Please note that any views or opinions presented in this email are solely those of the author and may not represent those of the Company or bind the Company. Any commitments made over e-mail are not financially binding on the company unless accompanied or followed by a valid purchase order. This message has been scanned for viruses and dangerous content by Mail Scanner, a! >> ?nd is believed to be clean. The Company accepts no liability for any damage caused by any virus transmitted by this email. >> www.jubl.com >> >> _______________________________________________ >> 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 > The information contained in this electronic message and in any attachments to this message is confidential, legally privileged and intended only for use by the person or entity to which this electronic message is addressed. If you are not the intended recipient, and have received this message in error, please notify the sender and system manager by return email and delete the message and its attachments and also you are hereby notified that any distribution, copying, review, retransmission, dissemination or other use of this electronic transmission or the information contained in it is strictly prohibited. Please note that any views or opinions presented in this email are solely those of the author and may not represent those of the Company or bind the Company. Any commitments made over e-mail are not financially binding on the company unless accompanied or followed by a valid purchase order. This message has been scanned for viruses and dangerous content by Mail Scanner, and is believed to be clean. The Company accepts no liability for any damage caused by any virus transmitted by this email. > www.jubl.com > The information contained in this electronic message and in any attachments to this message is confidential, legally privileged and intended only for use by the person or entity to which this electronic message is addressed. If you are not the intended recipient, and have received this message in error, please notify the sender and system manager by return email and delete the message and its attachments and also you are hereby notified that any distribution, copying, review, retransmission, dissemination or other use of this electronic transmission or the information contained in it is strictly prohibited. Please note that any views or opinions presented in this email are solely those of the author and may not represent those of the Company or bind the Company. Any commitments made over e-mail are not financially binding on the company unless accompanied or followed by a valid purchase order. This message has been scanned for viruses and dangerous content by Mail Scanner, and is believed to be clean. The Company accepts no liability for any damage caused by any virus transmitted by this email. www.jubl.com
ADD REPLY
0
Entering edit mode
On Thu, May 3, 2012 at 9:42 PM, Ekta Jain <ekta_jain at="" jubilantbiosys.com=""> wrote: > Hi Dan, > Found the windows package at http://bioc.ism.ac.jp/2.8/data/annotation/html/lumiHumanIDMapping.html > > I am going to download and use this as a locally downloaded package. It is version 1.10 which I think is the latest version? The type="source" flag to biocLite() installs the .tar.gz (source) package, or at least it is supposed to. I'm not sure why it isn't working for you. The link you sent above says the version is 1.10.0. Dan > > Regards, > Ekta > > -----Original Message----- > From: Dan Tenenbaum [mailto:dtenenba at fhcrc.org] > Sent: 04 May 2012 09:25 > To: Ekta Jain > Cc: bioconductor at r-project.org > Subject: Re: [BioC] lumiHumanIDMapping package does not exist for windows? > > On Thu, May 3, 2012 at 8:35 PM, Ekta Jain <ekta_jain at="" jubilantbiosys.com=""> wrote: >> Dear Dan, >> That wouldn't work as well. If we don't have the package available on Bioconductor.org then biocLite will not be able to download it. >> > > What is the exact error message, and the output of sessionInfo()? > > Also what is the output of > ?getOption("BioC_mirror") > ? > >> I did originally start with the way you suggested. When it didn't work thought of downloading the relevant .gz file from Bioconductor, which is not available. >> > > > The .gz file is available, see the you emailed. However, biocLite() is > the preferred way to install it, so let's figure out why that is not > working. > Dan > > >> Any help would be great !!! >> >> Thanks, >> Ekta >> >> -----Original Message----- >> From: Dan Tenenbaum [mailto:dtenenba at fhcrc.org] >> Sent: 03 May 2012 23:22 >> To: Ekta Jain >> Cc: bioconductor at r-project.org >> Subject: Re: [BioC] lumiHumanIDMapping package does not exist for windows? >> >> On Thu, May 3, 2012 at 4:39 AM, Ekta Jain <ekta_jain at="" jubilantbiosys.com=""> wrote: >>> Dear All, >>> The lumiHumanIDMapping package does not seem to have the windows binary files available on the Bioconductor website - http://www.biocon ductor.org/packages/release/data/annotation/html/lumiHumanIDMapping.ht ml >>> >>> Can anyone please tell me where i can get the same .gz package from? >> >> I'll look into why this is not available for windows, but in the >> meantime you can install it as follows: >> >> source("http://bioconductor.org/biocLite.R") >> biocLite("lumiHumanIDMapping", type="source") >> >> Dan >> >>> >>> Many Thanks, >>> Ekta >>> Senior Research Associate >>> Bioinformatics Department >>> Jubilant Biosys Pvt Ltd, >>> #96, Industrial Suburb, 2nd Stage >>> Yeshwantpur, Bangalore 560 022 >>> Ph No : +91-80-66628346 >>> >>> >>> The information contained in this electronic message and in any attachments to this message is confidential, legally privileged and intended only for use by the person or entity to which this electronic message is addressed. If you are not the intended recipient, and have received this message in error, please notify the sender and system manager by return email and delete the message and its attachments and also you are hereby notified that any distribution, copying, review, retransmission, dissemination or other use of this electronic transmission or the information contained in it is strictly prohibited. Please note that any views or opinions presented in this email are solely those of the author and may not represent those of the Company or bind the Company. Any commitments made over e-mail are not financially binding on the company unless accompanied or followed by a valid purchase order. This message has been scanned for viruses and dangerous content by Mail Scanner, a! >>> ?nd is believed to be clean. The Company accepts no liability for any damage caused by any virus transmitted by this email. >>> www.jubl.com >>> >>> _______________________________________________ >>> 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 >> The information contained in this electronic message and in any attachments to this message is confidential, legally privileged and intended only for use by the person or entity to which this electronic message is addressed. If you are not the intended recipient, and have received this message in error, please notify the sender and system manager by return email and delete the message and its attachments and also you are hereby notified that any distribution, copying, review, retransmission, dissemination or other use of this electronic transmission or the information contained in it is strictly prohibited. Please note that any views or opinions presented in this email are solely those of the author and may not represent those of the Company or bind the Company. Any commitments made over e-mail are not financially binding on the company unless accompanied or followed by a valid purchase order. This message has been scanned for viruses and dangerous content by Mail Scanner, and is believed to be clean. The Company accepts no liability for any damage caused by any virus transmitted by this email. >> www.jubl.com >> > The information contained in this electronic message and in any attachments to this message is confidential, legally privileged and intended only for use by the person or entity to which this electronic message is addressed. If you are not the intended recipient, and have received this message in error, please notify the sender and system manager by return email and delete the message and its attachments and also you are hereby notified that any distribution, copying, review, retransmission, dissemination or other use of this electronic transmission or the information contained in it is strictly prohibited. Please note that any views or opinions presented in this email are solely those of the author and may not represent those of the Company or bind the Company. Any commitments made over e-mail are not financially binding on the company unless accompanied or followed by a valid purchase order. This message has been scanned for viruses and dangerous content by Mail Scanner, and is believed to be clean. The Company accepts no liability for any damage caused by any virus transmitted by this email. > www.jubl.com >
ADD REPLY
0
Entering edit mode
Hi Dan, The tar.gz works on linux and a separate .gz file must be there for it to work on window. Correct me if i am wrong here but as far as i have seen most packages have both tar.gz and .gz files the former for linux based systems and the latter for windows machines. Ekta -----Original Message----- From: Dan Tenenbaum [mailto:dtenenba@fhcrc.org] Sent: 04 May 2012 10:17 To: Ekta Jain Cc: bioconductor at r-project.org Subject: Re: [BioC] lumiHumanIDMapping package does not exist for windows? On Thu, May 3, 2012 at 9:42 PM, Ekta Jain <ekta_jain at="" jubilantbiosys.com=""> wrote: > Hi Dan, > Found the windows package at http://bioc.ism.ac.jp/2.8/data/annotation/html/lumiHumanIDMapping.html > > I am going to download and use this as a locally downloaded package. It is version 1.10 which I think is the latest version? The type="source" flag to biocLite() installs the .tar.gz (source) package, or at least it is supposed to. I'm not sure why it isn't working for you. The link you sent above says the version is 1.10.0. Dan > > Regards, > Ekta > > -----Original Message----- > From: Dan Tenenbaum [mailto:dtenenba at fhcrc.org] > Sent: 04 May 2012 09:25 > To: Ekta Jain > Cc: bioconductor at r-project.org > Subject: Re: [BioC] lumiHumanIDMapping package does not exist for windows? > > On Thu, May 3, 2012 at 8:35 PM, Ekta Jain <ekta_jain at="" jubilantbiosys.com=""> wrote: >> Dear Dan, >> That wouldn't work as well. If we don't have the package available on Bioconductor.org then biocLite will not be able to download it. >> > > What is the exact error message, and the output of sessionInfo()? > > Also what is the output of > ?getOption("BioC_mirror") > ? > >> I did originally start with the way you suggested. When it didn't work thought of downloading the relevant .gz file from Bioconductor, which is not available. >> > > > The .gz file is available, see the you emailed. However, biocLite() is > the preferred way to install it, so let's figure out why that is not > working. > Dan > > >> Any help would be great !!! >> >> Thanks, >> Ekta >> >> -----Original Message----- >> From: Dan Tenenbaum [mailto:dtenenba at fhcrc.org] >> Sent: 03 May 2012 23:22 >> To: Ekta Jain >> Cc: bioconductor at r-project.org >> Subject: Re: [BioC] lumiHumanIDMapping package does not exist for windows? >> >> On Thu, May 3, 2012 at 4:39 AM, Ekta Jain <ekta_jain at="" jubilantbiosys.com=""> wrote: >>> Dear All, >>> The lumiHumanIDMapping package does not seem to have the windows binary files available on the Bioconductor website - http://www.biocon ductor.org/packages/release/data/annotation/html/lumiHumanIDMapping.ht ml >>> >>> Can anyone please tell me where i can get the same .gz package from? >> >> I'll look into why this is not available for windows, but in the >> meantime you can install it as follows: >> >> source("http://bioconductor.org/biocLite.R") >> biocLite("lumiHumanIDMapping", type="source") >> >> Dan >> >>> >>> Many Thanks, >>> Ekta >>> Senior Research Associate >>> Bioinformatics Department >>> Jubilant Biosys Pvt Ltd, >>> #96, Industrial Suburb, 2nd Stage >>> Yeshwantpur, Bangalore 560 022 >>> Ph No : +91-80-66628346 > The information contained in this electronic message and in any attachments to this message is confidential, legally privileged and intended only for use by the person or entity to which this electronic message is addressed. If you are not the intended recipient, and have received this message in error, please notify the sender and system manager by return email and delete the message and its attachments and also you are hereby notified that any distribution, copying, review, retransmission, dissemination or other use of this electronic transmission or the information contained in it is strictly prohibited. Please note that any views or opinions presented in this email are solely those of the author and may not represent those of the Company or bind the Company. Any commitments made over e-mail are not financially binding on the company unless accompanied or followed by a valid purchase order. This message has been scanned for viruses and dangerous content by Mail Scanner, and is believed to be clean. The Company accepts no liability for any damage caused by any virus transmitted by this email. www.jubl.com
ADD REPLY
0
Entering edit mode
On Thu, May 3, 2012 at 9:59 PM, Ekta Jain <ekta_jain at="" jubilantbiosys.com=""> wrote: > Hi Dan, > The tar.gz works on linux and a separate .gz file must be there for it to work on window. Correct me if i am wrong You are wrong. ;) tar.gz is the source package type, and the appropriate type for linux, but will install on any platform if you specify type="source" in your biocLite() command. .tgz is the extension for native Mac packages and .zip is the extension for native windows packages. Dan >here but as far as i have seen most packages have both tar.gz and .gz files the former for linux based systems and the latter for windows machines. > > Ekta > > -----Original Message----- > From: Dan Tenenbaum [mailto:dtenenba at fhcrc.org] > Sent: 04 May 2012 10:17 > To: Ekta Jain > Cc: bioconductor at r-project.org > Subject: Re: [BioC] lumiHumanIDMapping package does not exist for windows? > > On Thu, May 3, 2012 at 9:42 PM, Ekta Jain <ekta_jain at="" jubilantbiosys.com=""> wrote: >> Hi Dan, >> Found the windows package at http://bioc.ism.ac.jp/2.8/data/annotation/html/lumiHumanIDMapping.html >> >> I am going to download and use this as a locally downloaded package. It is version 1.10 which I think is the latest version? > > > The type="source" flag to biocLite() installs the .tar.gz (source) > package, or at least it is supposed to. I'm not sure why it isn't > working for you. > > The link you sent above says the version is 1.10.0. > > Dan > > > > >> >> Regards, >> Ekta >> >> -----Original Message----- >> From: Dan Tenenbaum [mailto:dtenenba at fhcrc.org] >> Sent: 04 May 2012 09:25 >> To: Ekta Jain >> Cc: bioconductor at r-project.org >> Subject: Re: [BioC] lumiHumanIDMapping package does not exist for windows? >> >> On Thu, May 3, 2012 at 8:35 PM, Ekta Jain <ekta_jain at="" jubilantbiosys.com=""> wrote: >>> Dear Dan, >>> That wouldn't work as well. If we don't have the package available on Bioconductor.org then biocLite will not be able to download it. >>> >> >> What is the exact error message, and the output of sessionInfo()? >> >> Also what is the output of >> ?getOption("BioC_mirror") >> ? >> >>> I did originally start with the way you suggested. When it didn't work thought of downloading the relevant .gz file from Bioconductor, which is not available. >>> >> >> >> The .gz file is available, see the you emailed. However, biocLite() is >> the preferred way to install it, so let's figure out why that is not >> working. >> Dan >> >> >>> Any help would be great !!! >>> >>> Thanks, >>> Ekta >>> >>> -----Original Message----- >>> From: Dan Tenenbaum [mailto:dtenenba at fhcrc.org] >>> Sent: 03 May 2012 23:22 >>> To: Ekta Jain >>> Cc: bioconductor at r-project.org >>> Subject: Re: [BioC] lumiHumanIDMapping package does not exist for windows? >>> >>> On Thu, May 3, 2012 at 4:39 AM, Ekta Jain <ekta_jain at="" jubilantbiosys.com=""> wrote: >>>> Dear All, >>>> The lumiHumanIDMapping package does not seem to have the windows binary files available on the Bioconductor website - http://www.biocon ductor.org/packages/release/data/annotation/html/lumiHumanIDMapping.ht ml >>>> >>>> Can anyone please tell me where i can get the same .gz package from? >>> >>> I'll look into why this is not available for windows, but in the >>> meantime you can install it as follows: >>> >>> source("http://bioconductor.org/biocLite.R") >>> biocLite("lumiHumanIDMapping", type="source") >>> >>> Dan >>> >>>> >>>> Many Thanks, >>>> Ekta >>>> Senior Research Associate >>>> Bioinformatics Department >>>> Jubilant Biosys Pvt Ltd, >>>> #96, Industrial Suburb, 2nd Stage >>>> Yeshwantpur, Bangalore 560 022 >>>> Ph No : +91-80-66628346 >> > The information contained in this electronic message and in any attachments to this message is confidential, legally privileged and intended only for use by the person or entity to which this electronic message is addressed. If you are not the intended recipient, and have received this message in error, please notify the sender and system manager by return email and delete the message and its attachments and also you are hereby notified that any distribution, copying, review, retransmission, dissemination or other use of this electronic transmission or the information contained in it is strictly prohibited. Please note that any views or opinions presented in this email are solely those of the author and may not represent those of the Company or bind the Company. Any commitments made over e-mail are not financially binding on the company unless accompanied or followed by a valid purchase order. This message has been scanned for viruses and dangerous content by Mail Scanner, and is believed to be clean. The Company accepts no liability for any damage caused by any virus transmitted by this email. > www.jubl.com >
ADD REPLY
0
Entering edit mode
Hi Dan, Thanks for that info :) I am clueless as to why it wouldn't then install it from biocLite. I've got it working in R anyway so will proceed using what I have from the previous link. Thank you for your time here. Regards, -E -----Original Message----- From: Dan Tenenbaum [mailto:dtenenba@fhcrc.org] Sent: 04 May 2012 10:40 To: Ekta Jain Cc: bioconductor at r-project.org Subject: Re: [BioC] lumiHumanIDMapping package does not exist for windows? On Thu, May 3, 2012 at 9:59 PM, Ekta Jain <ekta_jain at="" jubilantbiosys.com=""> wrote: > Hi Dan, > The tar.gz works on linux and a separate .gz file must be there for it to work on window. Correct me if i am wrong You are wrong. ;) tar.gz is the source package type, and the appropriate type for linux, but will install on any platform if you specify type="source" in your biocLite() command. .tgz is the extension for native Mac packages and .zip is the extension for native windows packages. Dan >here but as far as i have seen most packages have both tar.gz and .gz files the former for linux based systems and the latter for windows machines. > > Ekta > > -----Original Message----- > From: Dan Tenenbaum [mailto:dtenenba at fhcrc.org] > Sent: 04 May 2012 10:17 > To: Ekta Jain > Cc: bioconductor at r-project.org > Subject: Re: [BioC] lumiHumanIDMapping package does not exist for windows? > > On Thu, May 3, 2012 at 9:42 PM, Ekta Jain <ekta_jain at="" jubilantbiosys.com=""> wrote: >> Hi Dan, >> Found the windows package at http://bioc.ism.ac.jp/2.8/data/annotation/html/lumiHumanIDMapping.html >> >> I am going to download and use this as a locally downloaded package. It is version 1.10 which I think is the latest version? > > > The type="source" flag to biocLite() installs the .tar.gz (source) > package, or at least it is supposed to. I'm not sure why it isn't > working for you. > > The link you sent above says the version is 1.10.0. > > Dan > > > > >> >> Regards, >> Ekta >> >> -----Original Message----- >> From: Dan Tenenbaum [mailto:dtenenba at fhcrc.org] >> Sent: 04 May 2012 09:25 >> To: Ekta Jain >> Cc: bioconductor at r-project.org >> Subject: Re: [BioC] lumiHumanIDMapping package does not exist for windows? >> >> On Thu, May 3, 2012 at 8:35 PM, Ekta Jain <ekta_jain at="" jubilantbiosys.com=""> wrote: >>> Dear Dan, >>> That wouldn't work as well. If we don't have the package available on Bioconductor.org then biocLite will not be able to download it. >>> >> >> What is the exact error message, and the output of sessionInfo()? >> >> Also what is the output of >> ?getOption("BioC_mirror") >> ? >> >>> I did originally start with the way you suggested. When it didn't work thought of downloading the relevant .gz file from Bioconductor, which is not available. >>> >> >> >> The .gz file is available, see the you emailed. However, biocLite() is >> the preferred way to install it, so let's figure out why that is not >> working. >> Dan >> >> >>> Any help would be great !!! >>> >>> Thanks, >>> Ekta >>> >>> -----Original Message----- >>> From: Dan Tenenbaum [mailto:dtenenba at fhcrc.org] >>> Sent: 03 May 2012 23:22 >>> To: Ekta Jain >>> Cc: bioconductor at r-project.org >>> Subject: Re: [BioC] lumiHumanIDMapping package does not exist for windows? >>> >>> On Thu, May 3, 2012 at 4:39 AM, Ekta Jain <ekta_jain at="" jubilantbiosys.com=""> wrote: >>>> Dear All, >>>> The lumiHumanIDMapping package does not seem to have the windows binary files available on the Bioconductor website - http://www.biocon ductor.org/packages/release/data/annotation/html/lumiHumanIDMapping.ht ml >>>> >>>> Can anyone please tell me where i can get the same .gz package from? >>> >>> I'll look into why this is not available for windows, but in the >>> meantime you can install it as follows: >>> >>> source("http://bioconductor.org/biocLite.R") >>> biocLite("lumiHumanIDMapping", type="source") >>> >>> Dan >>> >>>> >>>> Many Thanks, >>>> Ekta >>>> Senior Research Associate >>>> Bioinformatics Department >>>> Jubilant Biosys Pvt Ltd, >>>> #96, Industrial Suburb, 2nd Stage >>>> Yeshwantpur, Bangalore 560 022 >>>> Ph No : +91-80-66628346 >> > The information contained in this electronic message and in any attachments to this message is confidential, legally privileged and intended only for use by the person or entity to which this electronic message is addressed. If you are not the intended recipient, and have received this message in error, please notify the sender and system manager by return email and delete the message and its attachments and also you are hereby notified that any distribution, copying, review, retransmission, dissemination or other use of this electronic transmission or the information contained in it is strictly prohibited. Please note that any views or opinions presented in this email are solely those of the author and may not represent those of the Company or bind the Company. Any commitments made over e-mail are not financially binding on the company unless accompanied or followed by a valid purchase order. This message has been scanned for viruses and dangerous content by Mail Scanner, and is believed to be clean. The Company accepts no liability for any damage caused by any virus transmitted by this email. > www.jubl.com > The information contained in this electronic message and in any attachments to this message is confidential, legally privileged and intended only for use by the person or entity to which this electronic message is addressed. If you are not the intended recipient, and have received this message in error, please notify the sender and system manager by return email and delete the message and its attachments and also you are hereby notified that any distribution, copying, review, retransmission, dissemination or other use of this electronic transmission or the information contained in it is strictly prohibited. Please note that any views or opinions presented in this email are solely those of the author and may not represent those of the Company or bind the Company. Any commitments made over e-mail are not financially binding on the company unless accompanied or followed by a valid purchase order. This message has been scanned for viruses and dangerous content by Mail Scanner, and is believed to be clean. The Company accepts no liability for any damage caused by any virus transmitted by this email. www.jubl.com
ADD REPLY

Login before adding your answer.

Traffic: 622 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6