
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 Rodrķguez [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 āupListā 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 āupListā 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





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