Question: help with SCAN.UPC and u133aaofav2
0
gravatar for Juliet Hannah
6.1 years ago by
Juliet Hannah360
United States
Juliet Hannah360 wrote:
All, I am trying to run scan and I obtain the following error. I searched for the packages (pd.u133aaofav2), could not find them, and I'm confused about how to proceed: # command used normalized = SCAN("myCEL.CEL") # error message Loading required package: pd.u133aaofav2 Attempting to obtain 'pd.u133aaofav2' from BioConductor website. Checking to see if your internet connection works... Package 'pd.u133aaofav2' was not found in the BioConductor repository. The 'pdInfoBuilder' package can often be used in situations like this. Error in { : task 1 failed - "The annotation package, pd.u133aaofav2, could not be loaded." In addition: Warning messages: 1: executing %dopar% sequentially: no parallel backend registered 2: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : there is no package called âpd.u133aaofav2â # sessionInfo() R version 3.0.2 (2013-09-25) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] parallel stats graphics grDevices utils datasets methods [8] base other attached packages: [1] SCAN.UPC_2.4.0 foreach_1.4.1 affyio_1.30.0 [4] affy_1.40.0 GEOquery_2.28.0 Biostrings_2.30.0 [7] XVector_0.2.0 IRanges_1.20.4 oligo_1.26.0 [10] oligoClasses_1.24.0 Biobase_2.22.0 BiocGenerics_0.8.0 loaded via a namespace (and not attached): [1] affxparser_1.34.0 BiocInstaller_1.12.0 bit_1.1-10 [4] codetools_0.2-8 compiler_3.0.2 DBI_0.2-7 [7] ff_2.2-12 GenomicRanges_1.14.3 iterators_1.0.6 [10] MASS_7.3-29 preprocessCore_1.24.0 RCurl_1.95-4.1 [13] splines_3.0.2 stats4_3.0.2 tools_3.0.2 [16] XML_3.98-1.1 zlibbioc_1.8.0 [[alternative HTML version deleted]]
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ADD COMMENTlink modified 6.1 years ago by Stephen Piccolo560 • written 6.1 years ago by Juliet Hannah360
Answer: help with SCAN.UPC and u133aaofav2
0
gravatar for Stephen Piccolo
6.1 years ago by
United States
Stephen Piccolo560 wrote:
Hi Juliet, Thanks for your question. You can get around this by using the "annotationPackageName" parameter to indicate an annotation package that describes the layout for these chips. I don't know of an annotation package specifically for these "early access" arrays. But from what I can tell, the layout of these chips is exactly the same as the HT U133A arrays (which superseded the EA arrays). So what you can do is indicate that you want to use the annotation package for the HT U133A arrays. Below is an example: Normalized = SCAN("myCEL.CEL", annotationPackageName="pd.ht.hg.u133a") You may need to install this package manually, or Bioconductor may take care of it for you automatically (I can't remember). The documentation describes more detail, but please let me know if you run into problems. Regards, -Steve ---------------------------------------------------------------------- ----- --------------- Stephen Piccolo, Ph.D. Postdoctoral Research Associate Affiliations: Division of Computational Biomedicine, Boston University School of Medicine Department of Pharmacology and Toxicology, University of Utah Twitter: @stevepiccolo ---------------------------------------------------------------------- ----- ---------------------------- From: Juliet Hannah <juliet.hannah@gmail.com> Date: Thursday, October 31, 2013 7:56 PM To: Bioconductor mailing list <bioconductor at="" r-project.org="">, "W. Evan Johnson" <wej at="" bu.edu="">, Stephen Piccolo <stephen.piccolo at="" hsc.utah.edu=""> Subject: help with SCAN.UPC and u133aaofav2 All, I am trying to run scan and I obtain the following error. I searched for the packages (pd.u133aaofav2), could not find them, and I'm confused about how to proceed: # command used normalized = SCAN("myCEL.CEL") # error message Loading required package: pd.u133aaofav2 Attempting to obtain 'pd.u133aaofav2' from BioConductor website. Checking to see if your internet connection works... Package 'pd.u133aaofav2' was not found in the BioConductor repository. The 'pdInfoBuilder' package can often be used in situations like this. Error in { : task 1 failed - "The annotation package, pd.u133aaofav2, could not be loaded." In addition: Warning messages: 1: executing %dopar% sequentially: no parallel backend registered 2: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : there is no package called ?pd.u133aaofav2? # sessionInfo() R version 3.0.2 (2013-09-25) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] parallel stats graphics grDevices utils datasets methods [8] base other attached packages: [1] SCAN.UPC_2.4.0 foreach_1.4.1 affyio_1.30.0 [4] affy_1.40.0 GEOquery_2.28.0 Biostrings_2.30.0 [7] XVector_0.2.0 IRanges_1.20.4 oligo_1.26.0 [10] oligoClasses_1.24.0 Biobase_2.22.0 BiocGenerics_0.8.0 loaded via a namespace (and not attached): [1] affxparser_1.34.0 BiocInstaller_1.12.0 bit_1.1-10 [4] codetools_0.2-8 compiler_3.0.2 DBI_0.2-7 [7] ff_2.2-12 GenomicRanges_1.14.3 iterators_1.0.6 [10] MASS_7.3-29 preprocessCore_1.24.0 RCurl_1.95-4.1 [13] splines_3.0.2 stats4_3.0.2 tools_3.0.2 [16] XML_3.98-1.1 zlibbioc_1.8.0
ADD COMMENTlink written 6.1 years ago by Stephen Piccolo560
Hi Steve, Thanks for responding. I am using the cmap data, which I believe was used in your SCAN paper. Did you you the three types of chips? Thanks, Juliet On Fri, Nov 1, 2013 at 10:53 AM, Steve Piccolo <stephen.piccolo@hsc.utah.edu> wrote: > Hi Juliet, > > Thanks for your question. > > You can get around this by using the "annotationPackageName" parameter to > indicate an annotation package that describes the layout for these chips. > I don't know of an annotation package specifically for these "early > access" arrays. But from what I can tell, the layout of these chips is > exactly the same as the HT U133A arrays (which superseded the EA arrays). > So what you can do is indicate that you want to use the annotation package > for the HT U133A arrays. > > Below is an example: > > Normalized = SCAN("myCEL.CEL", annotationPackageName="pd.ht.hg.u133a") > > You may need to install this package manually, or Bioconductor may take > care of it for you automatically (I can't remember). The documentation > describes more detail, but please let me know if you run into problems. > > Regards, > -Steve > > -------------------------------------------------------------------- ------- > --------------- > Stephen Piccolo, Ph.D. > Postdoctoral Research Associate > > Affiliations: > Division of Computational Biomedicine, Boston University School of > Medicine > > Department of Pharmacology and Toxicology, University of Utah > > Twitter: @stevepiccolo > -------------------------------------------------------------------- ------- > ---------------------------- > > > > > > > > From: Juliet Hannah <juliet.hannah@gmail.com> > Date: Thursday, October 31, 2013 7:56 PM > To: Bioconductor mailing list <bioconductor@r-project.org>, "W. Evan > Johnson" <wej@bu.edu>, Stephen Piccolo <stephen.piccolo@hsc.utah.edu> > Subject: help with SCAN.UPC and u133aaofav2 > > > All, > > I am trying to run scan and I obtain the following error. I searched for > the packages (pd.u133aaofav2), could not find them, and I'm confused about > how to proceed: > > > # command used > > normalized = SCAN("myCEL.CEL") > > # error message > > Loading required package: pd.u133aaofav2 > Attempting to obtain 'pd.u133aaofav2' from BioConductor website. > Checking to see if your internet connection works... > Package 'pd.u133aaofav2' was not found in the BioConductor repository. > The 'pdInfoBuilder' package can often be used in situations like this. > Error in { : > task 1 failed - "The annotation package, pd.u133aaofav2, could not be > loaded." > In addition: Warning messages: > 1: executing %dopar% sequentially: no parallel backend registered > 2: In library(package, lib.loc = lib.loc, character.only = TRUE, > logical.return = TRUE, : > there is no package called âpd.u133aaofav2â > > > > # sessionInfo() > > R version 3.0.2 (2013-09-25) > Platform: x86_64-unknown-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] parallel stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] SCAN.UPC_2.4.0 foreach_1.4.1 affyio_1.30.0 > [4] affy_1.40.0 GEOquery_2.28.0 Biostrings_2.30.0 > [7] XVector_0.2.0 IRanges_1.20.4 oligo_1.26.0 > [10] oligoClasses_1.24.0 Biobase_2.22.0 BiocGenerics_0.8.0 > > loaded via a namespace (and not attached): > [1] affxparser_1.34.0 BiocInstaller_1.12.0 bit_1.1-10 > [4] codetools_0.2-8 compiler_3.0.2 DBI_0.2-7 > [7] ff_2.2-12 GenomicRanges_1.14.3 iterators_1.0.6 > [10] MASS_7.3-29 preprocessCore_1.24.0 RCurl_1.95-4.1 > [13] splines_3.0.2 stats4_3.0.2 tools_3.0.2 > [16] XML_3.98-1.1 zlibbioc_1.8.0 > > [[alternative HTML version deleted]]
ADD REPLYlink written 6.1 years ago by Juliet Hannah360
Hi Juliet, For the SCAN paper, we used the Python version of the SCAN code. Since that time, I ported everything to R/Bioconductor. I have a colleague who recently needed to analyze u133aaofav2 arrays from CMAP, and the approach I described worked well for him with the Bioconductor version of SCAN. Thanks, -Steve From: Juliet Hannah <juliet.hannah@gmail.com<mailto:juliet.hannah@gmail.com>> Date: Friday, November 1, 2013 9:42 AM To: Stephen Piccolo <stephen.piccolo@hsc.utah.edu<mailto:stephen.piccolo@hsc.utah.edu>> Cc: Bioconductor mailing list <bioconductor@r-project.org<mailto:bioconductor@r-project.org>> Subject: Re: help with SCAN.UPC and u133aaofav2 Hi Steve, Thanks for responding. I am using the cmap data, which I believe was used in your SCAN paper. Did you you the three types of chips? Thanks, Juliet On Fri, Nov 1, 2013 at 10:53 AM, Steve Piccolo <stephen.piccolo@hsc.utah.edu<mailto:stephen.piccolo@hsc.utah.edu>> wrote: Hi Juliet, Thanks for your question. You can get around this by using the "annotationPackageName" parameter to indicate an annotation package that describes the layout for these chips. I don't know of an annotation package specifically for these "early access" arrays. But from what I can tell, the layout of these chips is exactly the same as the HT U133A arrays (which superseded the EA arrays). So what you can do is indicate that you want to use the annotation package for the HT U133A arrays. Below is an example: Normalized = SCAN("myCEL.CEL", annotationPackageName="pd.ht.hg.u133a") You may need to install this package manually, or Bioconductor may take care of it for you automatically (I can't remember). The documentation describes more detail, but please let me know if you run into problems. Regards, -Steve ---------------------------------------------------------------------- ----- --------------- Stephen Piccolo, Ph.D. Postdoctoral Research Associate Affiliations: Division of Computational Biomedicine, Boston University School of Medicine Department of Pharmacology and Toxicology, University of Utah Twitter: @stevepiccolo ---------------------------------------------------------------------- ----- ---------------------------- From: Juliet Hannah <juliet.hannah@gmail.com<mailto:juliet.hannah@gmail.com>> Date: Thursday, October 31, 2013 7:56 PM To: Bioconductor mailing list <bioconductor@r-project.org<mailto:bioconductor@r-project.org>>, "W. Evan Johnson" <wej@bu.edu<mailto:wej@bu.edu>>, Stephen Piccolo <stephen.piccolo@hsc.utah.edu<mailto:stephen.piccolo@hsc.utah.edu>> Subject: help with SCAN.UPC and u133aaofav2 All, I am trying to run scan and I obtain the following error. I searched for the packages (pd.u133aaofav2), could not find them, and I'm confused about how to proceed: # command used normalized = SCAN("myCEL.CEL") # error message Loading required package: pd.u133aaofav2 Attempting to obtain 'pd.u133aaofav2' from BioConductor website. Checking to see if your internet connection works... Package 'pd.u133aaofav2' was not found in the BioConductor repository. The 'pdInfoBuilder' package can often be used in situations like this. Error in { : task 1 failed - "The annotation package, pd.u133aaofav2, could not be loaded." In addition: Warning messages: 1: executing %dopar% sequentially: no parallel backend registered 2: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : there is no package called âpd.u133aaofav2â # sessionInfo() R version 3.0.2 (2013-09-25) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] parallel stats graphics grDevices utils datasets methods [8] base other attached packages: [1] SCAN.UPC_2.4.0 foreach_1.4.1 affyio_1.30.0 [4] affy_1.40.0 GEOquery_2.28.0 Biostrings_2.30.0 [7] XVector_0.2.0 IRanges_1.20.4 oligo_1.26.0 [10] oligoClasses_1.24.0 Biobase_2.22.0 BiocGenerics_0.8.0 loaded via a namespace (and not attached): [1] affxparser_1.34.0 BiocInstaller_1.12.0 bit_1.1-10 [4] codetools_0.2-8 compiler_3.0.2 DBI_0.2-7 [7] ff_2.2-12 GenomicRanges_1.14.3 iterators_1.0.6 [10] MASS_7.3-29 preprocessCore_1.24.0 RCurl_1.95-4.1 [13] splines_3.0.2 stats4_3.0.2 tools_3.0.2 [16] XML_3.98-1.1 zlibbioc_1.8.0 [[alternative HTML version deleted]]
ADD REPLYlink written 6.1 years ago by Stephen Piccolo560
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