Question: GO-Pathways using RDAVIDWebService
0
gravatar for Fazulur Rehaman
5.7 years ago by
Fazulur Rehaman50 wrote:
Dear Sir, I am trying to get Gene Ontology and Pathways for "Human Genome U133 Plus2..0 array" using RDAVIDWebService. But it giving for whole human genome. Here is the script I used: 1. addList function with 'Gene' as listType : I am getting results for whole genome and it selected Homo sapiens as available Background List. > upList <- up$Probe.Set.ID > data(upList) Warning message: In data(upList) : data set âupListâ not found > result <- addList(david,upList,"AFFYMETRIX_3PRIME_IVT_ID",listName = "Human Genome U133 Plus2.0 array",listType = "Gene") > david DAVIDWebService object to access DAVID's website. User email: fazulur.r@ocimumbio.com Available Gene List/s: Name Using 1 Human Genome U133 Plus2.0 array * Available Specie/s: Name Using 1 Homo sapiens(320) * Available Background List/s: Name Using 1 Homo sapiens * 2. addList function with 'Background' as listType : I am not getting any results after giving below command > result <- addList(david,upList,"AFFYMETRIX_3PRIME_IVT_ID",listName = "Human Genome U133 Plus2.0 array",listType = "Background") Would you please suggest me how to get GO&Pathways for particularly "Human Genome U133 Plus2.0 array". Regards Rehaman ________________________________ This e-mail contains PRIVILEGED AND CONFIDENTIAL INFORMATION intended solely for the use of the addressee(s). If you are not the intended recipient, please notify the sender by e-mail and delete the original message. Further, you are not to copy, disclose, or distribute this e-mail or its contents to any other person and any such actions that are unlawful. This e-mail may contain viruses. Ocimum Biosolutions has taken every reasonable precaution to minimize this risk, but is not liable for any damage you may sustain as a result of any virus in this e-mail. You should carry out your own virus checks before opening the e-mail or attachment. The information contained in this email and any attachments is confidential and may be subject to copyright or other intellectual property protection. If you are not the intended recipient, you are not authorized to use or disclose this information, and we request that you notify us by reply mail or telephone and delete the original message from your mail system. OCIMUMBIO SOLUTIONS (P) LTD [[alternative HTML version deleted]]
ADD COMMENTlink modified 5.7 years ago by Cristobal Fresno Rodríguez360 • written 5.7 years ago by Fazulur Rehaman50
Answer: GO-Pathways using RDAVIDWebService
0
gravatar for Cristobal Fresno Rodríguez
5.7 years ago by
Argentina/Cordoba/Universidad Católica de Córdoba (CONICET)
Hi Rehaman, Thanks for your interest in RDAVIDWebService. As regards your question, some points to take into account: - Calling *data(upList)* makes an error because upList is not included in any loaded package. > data(upList) Warning message: In data(upList) : data set âupListâ not found - You can perform the analysis using your gene list (*upList*) as you did, which shows that successfully 320 IDs were recognized by DAVID. Name Using 1 Human Genome U133 Plus2.0 array * Available Specie/s: Name Using *1 Homo sapiens(320) ** - About the Background, you can use: - The whole genome of the organism which is the default option as the output highlighted in red shows in your mail: Available Background List/s: Name Using 1 Homo sapiens * - Upload a user-defined background: - It won't do any good to upload here the same genes of the gene list, as you did: > result <- addList(david,upList,"AFFYMETRIX_3PRIME_IVT_ID",listName = "Human Genome U133 Plus2.0 array",listType = "Background") because both *listType="Gene"* and *listType="Background" *use the same genes of *upList* object. You could check the new status calling *david*object again. - Unfortunately, default chip backgrounds are not available by DAVID Web Service API. However, you could use "hgu133plus2.db" package and upload the complete printed gene list of the chip or using the annotation you used in your analysis. Let me know if you could solve your problem. Regards Cristobal Fresno 2014-02-12 7:55 GMT-03:00 Fazulur Rehaman <fazulur.r@ocimumbio.com>: > Dear Sir, > > > > I am trying to get Gene Ontology and Pathways for "Human Genome U133 > Plus2.0 array" using RDAVIDWebService. But it giving for whole human > genome. > > > > Here is the script I used: > > > > 1. addList function with 'Gene' as listType : I am getting results for > whole genome and it selected Homo sapiens as available Background List. > > > > > > > upList <- up$Probe.Set.ID > > > data(upList) > > Warning message: > > In data(upList) : data set âupListâ not found > > > result <- addList(david,upList,"AFFYMETRIX_3PRIME_IVT_ID",listName = > "Human Genome U133 Plus2.0 array",listType = "Gene") > > > david > > DAVIDWebService object to access DAVID's website. > > User email: fazulur.r@ocimumbio.com > > Available Gene List/s: > > Name Using > > 1 Human Genome U133 Plus2.0 array * > > Available Specie/s: > > Name Using > > 1 Homo sapiens(320) * > > Available Background List/s: > > Name Using > > 1 Homo sapiens * > > 2. addList function with 'Background' as listType : I am not getting any > results after giving below command > > > > > result <- addList(david,upList,"AFFYMETRIX_3PRIME_IVT_ID",listName = > "Human Genome U133 Plus2.0 array",listType = "Background") > > > > Would you please suggest me how to get GO&Pathways for particularly "Human > Genome U133 Plus2.0 array". > > > > Regards > > Rehaman > > > > > > > > > > ------------------------------ > This e-mail contains PRIVILEGED AND CONFIDENTIAL INFORMATION intended > solely for the use of the addressee(s). If you are not the intended > recipient, please notify the sender by e-mail and delete the original > message. Further, you are not to copy, disclose, or distribute this e-mail > or its contents to any other person and any such actions that are unlawful. > This e-mail may contain viruses. Ocimum Biosolutions has taken every > reasonable precaution to minimize this risk, but is not liable for any > damage you may sustain as a result of any virus in this e-mail. You should > carry out your own virus checks before opening the e-mail or attachment. > The information contained in this email and any attachments is > confidential and may be subject to copyright or other intellectual property > protection. If you are not the intended recipient, you are not authorized > to use or disclose this information, and we request that you notify us by > reply mail or telephone and delete the original message from your mail > system. > > OCIMUMBIO SOLUTIONS (P) LTD > [[alternative HTML version deleted]]
ADD COMMENTlink written 5.7 years ago by Cristobal Fresno Rodríguez360
Dear Dr. Cristobal Fresno, Thank's for giving me quick reply and sure I will let you know once I will done with this problem. Regards Rehaman From: Cristobal Fresno Rodr�guez [mailto:cristobalfresno@gmail.com] Sent: Wednesday, February 12, 2014 5:25 PM To: Fazulur Rehaman Cc: bioconductor@r-project.org Subject: Re: GO-Pathways using RDAVIDWebService Hi Rehaman, Thanks for your interest in RDAVIDWebService. As regards your question, some points to take into account: * Calling data(upList) makes an error because upList is not included in any loaded package. > data(upList) Warning message: In data(upList) : data set �upList� not found * You can perform the analysis using your gene list (upList) as you did, which shows that successfully 320 IDs were recognized by DAVID. Name Using 1 Human Genome U133 Plus2.0 array * Available Specie/s: Name Using 1 Homo sapiens(320) * * About the Background, you can use: * The whole genome of the organism which is the default option as the output highlighted in red shows in your mail: Available Background List/s: Name Using 1 Homo sapiens * o Upload a user-defined background: � It won't do any good to upload here the same genes of the gene list, as you did: > result <- addList(david,upList,"AFFYMETRIX_3PRIME_IVT_ID",listName = "Human Genome U133 Plus2.0 array",listType = "Background") because both listType="Gene" and listType="Background" use the same genes of upList object. You could check the new status calling david object again. * Unfortunately, default chip backgrounds are not available by DAVID Web Service API. However, you could use "hgu133plus2.db" package and upload the complete printed gene list of the chip or using the annotation you used in your analysis. Let me know if you could solve your problem. Regards Cristobal Fresno 2014-02-12 7:55 GMT-03:00 Fazulur Rehaman <fazulur.r@ocimumbio.com<mailto:fazulur.r@ocimumbio.com>>: Dear Sir, I am trying to get Gene Ontology and Pathways for "Human Genome U133 Plus2..0 array" using RDAVIDWebService. But it giving for whole human genome. Here is the script I used: 1. addList function with 'Gene' as listType : I am getting results for whole genome and it selected Homo sapiens as available Background List. > upList <- up$Probe.Set.ID<http: probe.set.id=""> > data(upList) Warning message: In data(upList) : data set �upList� not found > result <- addList(david,upList,"AFFYMETRIX_3PRIME_IVT_ID",listName = "Human Genome U133 Plus2.0 array",listType = "Gene") > david DAVIDWebService object to access DAVID's website. User email: fazulur.r@ocimumbio.com<mailto:fazulur.r@ocimumbio.com> Available Gene List/s: Name Using 1 Human Genome U133 Plus2.0 array * Available Specie/s: Name Using 1 Homo sapiens(320) * Available Background List/s: Name Using 1 Homo sapiens * 2. addList function with 'Background' as listType : I am not getting any results after giving below command > result <- addList(david,upList,"AFFYMETRIX_3PRIME_IVT_ID",listName = "Human Genome U133 Plus2.0 array",listType = "Background") Would you please suggest me how to get GO&Pathways for particularly "Human Genome U133 Plus2.0 array". Regards Rehaman ________________________________ This e-mail contains PRIVILEGED AND CONFIDENTIAL INFORMATION intended solely for the use of the addressee(s). If you are not the intended recipient, please notify the sender by e-mail and delete the original message. Further, you are not to copy, disclose, or distribute this e-mail or its contents to any other person and any such actions that are unlawful. This e-mail may contain viruses. Ocimum Biosolutions has taken every reasonable precaution to minimize this risk, but is not liable for any damage you may sustain as a result of any virus in this e-mail. You should carry out your own virus checks before opening the e-mail or attachment. The information contained in this email and any attachments is confidential and may be subject to copyright or other intellectual property protection. If you are not the intended recipient, you are not authorized to use or disclose this information, and we request that you notify us by reply mail or telephone and delete the original message from your mail system. OCIMUMBIO SOLUTIONS (P) LTD ________________________________ This e-mail contains PRIVILEGED AND CONFIDENTIAL INFORMATION intended solely for the use of the addressee(s). If you are not the intended recipient, please notify the sender by e-mail and delete the original message. Further, you are not to copy, disclose, or distribute this e-mail or its contents to any other person and any such actions that are unlawful. This e-mail may contain viruses. Ocimum Biosolutions has taken every reasonable precaution to minimize this risk, but is not liable for any damage you may sustain as a result of any virus in this e-mail. You should carry out your own virus checks before opening the e-mail or attachment. The information contained in this email and any attachments is confidential and may be subject to copyright or other intellectual property protection. If you are not the intended recipient, you are not authorized to use or disclose this information, and we request that you notify us by reply mail or telephone and delete the original message from your mail system. OCIMUMBIO SOLUTIONS (P) LTD [[alternative HTML version deleted]]
ADD REPLYlink written 5.7 years ago by Fazulur Rehaman50
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