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]]
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
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
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transmitted by this email.
www.jubl.com
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,
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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
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
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manager by return email and delete the message and its attachments and
also you are hereby notified that any distribution, copying, review,
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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
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
>
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
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
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
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message is addressed. If you are not the intended recipient, and have
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and dangerous content by Mail Scanner, a!
>>> ?nd is believed to be clean. The Company accepts no liability for
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>>> www.jubl.com
>>>
>>> _______________________________________________
>>> Bioconductor mailing list
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>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>> Search the archives:
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>> 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
>
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
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
>
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
