Question: Agilent Array Analysis Question
0
gravatar for Sunny Srivastava
9.9 years ago by
Sunny Srivastava340 wrote:
Dear Bioconductor Helpers, I have used Bioconductor to analyze Affy chips only, but recently I have to do some analysis for Agilent array. Each array has the two chips with the same sample but the dye swapped (I just made it clear as I saw most of the literature on such arrays with 4 chips). Can any one help me how to: 1 - Import data in Bioconductor? (I mean what is the equivalent of .cel files here - if there is any? I have a few .xml .csv, .txt and .shp files - I am clueless which ones to use and how should I use) 2 - I saw two packages - AgiMicroRNA and Agi4x44PreProcess (the latter seems to be for the 4 chip Agilent array) related to Agilent arrays. Can anyone point out a good article to read on - how to (completely) analyze such Agilent Arrays - importing, "cleaning up" and analyzing data? 3 - I saw Limma talks about dye swap analysis, so I guess I can use Limma to analyze this data after I am done importing data correctly. I am sorry if I used Agilent array/chip in a wrong way, my knowledge is very limited in this area. I have only analyzed Affy arrays until now. Any help will be appreciated. Thanks, S. [[alternative HTML version deleted]]
ADD COMMENTlink modified 9.9 years ago by Francois Pepin1.3k • written 9.9 years ago by Sunny Srivastava340
Answer: Agilent Array Analysis Question
0
gravatar for Francois Pepin
9.9 years ago by
Francois Pepin1.3k
Francois Pepin1.3k wrote:
Hi Sunny, To answer the questions in reverse order: 3- Yes, Limma is a good choice for it. The user's guide is long but full of extremely useful information. Going through the relevant sections is strongly recommended. 2- Agi4x44PreProcess works well if you have human or mouse 4x44 whole genome arrays. ArrayQualityMetrics will work anyway. Limma has some functions and suggestions as well for that. Again, the Limma user guide is a excellent place to start. 1- Did I mention Limma before? It read.maimages can read the .txt file from the extraction software. There are of course several ways of doing each of these steps. I mostly recommend limma for these steps as it is a reliable and well- documented package that should help you get started. Most of the analysis after normalization can be done similarly on Agilent and Affy chips. Francois On 11/19/2009 10:56 PM, Sunny Srivastava wrote: > Dear Bioconductor Helpers, > I have used Bioconductor to analyze Affy chips only, but recently I have to > do some analysis for Agilent array. Each array has the two chips with the > same sample but the dye swapped (I just made it clear as I saw most of the > literature on such arrays with 4 chips). > > Can any one help me how to: > 1 - Import data in Bioconductor? (I mean what is the equivalent of .cel > files here - if there is any? I have a few .xml .csv, .txt and .shp files - > I am clueless which ones to use and how should I use) > 2 - I saw two packages - AgiMicroRNA and Agi4x44PreProcess (the latter seems > to be for the 4 chip Agilent array) related to Agilent arrays. > Can anyone point out a good article to read on - how to (completely) > analyze such Agilent Arrays - importing, "cleaning up" and analyzing data? > 3 - I saw Limma talks about dye swap analysis, so I guess I can use Limma to > analyze this data after I am done importing data correctly. > > I am sorry if I used Agilent array/chip in a wrong way, my knowledge is very > limited in this area. I have only analyzed Affy arrays until now. > > Any help will be appreciated. > > Thanks, > S. > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD COMMENTlink written 9.9 years ago by Francois Pepin1.3k
Dear Mr. Pepin, Thanks a lot for your prompt reply. I saw the read.maimages but just wasn't sure which file to import. I will give it a try. Regards, S. On Thu, Nov 19, 2009 at 11:20 PM, Francois Pepin <fpepin@cs.mcgill.ca>wrote: > Hi Sunny, > > To answer the questions in reverse order: > > 3- Yes, Limma is a good choice for it. The user's guide is long but full of > extremely useful information. Going through the relevant sections is > strongly recommended. > 2- Agi4x44PreProcess works well if you have human or mouse 4x44 whole > genome arrays. ArrayQualityMetrics will work anyway. Limma has some > functions and suggestions as well for that. Again, the Limma user guide is a > excellent place to start. > 1- Did I mention Limma before? It read.maimages can read the .txt file from > the extraction software. > > There are of course several ways of doing each of these steps. I mostly > recommend limma for these steps as it is a reliable and well- documented > package that should help you get started. Most of the analysis after > normalization can be done similarly on Agilent and Affy chips. > > Francois > > > On 11/19/2009 10:56 PM, Sunny Srivastava wrote: > >> Dear Bioconductor Helpers, >> I have used Bioconductor to analyze Affy chips only, but recently I have >> to >> do some analysis for Agilent array. Each array has the two chips with the >> same sample but the dye swapped (I just made it clear as I saw most of the >> literature on such arrays with 4 chips). >> >> Can any one help me how to: >> 1 - Import data in Bioconductor? (I mean what is the equivalent of .cel >> files here - if there is any? I have a few .xml .csv, .txt and .shp files >> - >> I am clueless which ones to use and how should I use) >> 2 - I saw two packages - AgiMicroRNA and Agi4x44PreProcess (the latter >> seems >> to be for the 4 chip Agilent array) related to Agilent arrays. >> Can anyone point out a good article to read on - how to (completely) >> analyze such Agilent Arrays - importing, "cleaning up" and analyzing data? >> 3 - I saw Limma talks about dye swap analysis, so I guess I can use Limma >> to >> analyze this data after I am done importing data correctly. >> >> I am sorry if I used Agilent array/chip in a wrong way, my knowledge is >> very >> limited in this area. I have only analyzed Affy arrays until now. >> >> Any help will be appreciated. >> >> Thanks, >> S. >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
ADD REPLYlink written 9.9 years ago by Sunny Srivastava340
Thanks a lot !! Everything went pretty well .. I hope the analysis also goes smoothly :D Best Regards, S. On Thu, Nov 19, 2009 at 11:36 PM, Sunny Srivastava <research.baba@gmail.com>wrote: > Dear Mr. Pepin, > > Thanks a lot for your prompt reply. I saw the read.maimages but just wasn't > sure which file to import. > > I will give it a try. > > Regards, > S. > > > On Thu, Nov 19, 2009 at 11:20 PM, Francois Pepin <fpepin@cs.mcgill.ca>wrote: > >> Hi Sunny, >> >> To answer the questions in reverse order: >> >> 3- Yes, Limma is a good choice for it. The user's guide is long but full >> of extremely useful information. Going through the relevant sections is >> strongly recommended. >> 2- Agi4x44PreProcess works well if you have human or mouse 4x44 whole >> genome arrays. ArrayQualityMetrics will work anyway. Limma has some >> functions and suggestions as well for that. Again, the Limma user guide is a >> excellent place to start. >> 1- Did I mention Limma before? It read.maimages can read the .txt file >> from the extraction software. >> >> There are of course several ways of doing each of these steps. I mostly >> recommend limma for these steps as it is a reliable and well- documented >> package that should help you get started. Most of the analysis after >> normalization can be done similarly on Agilent and Affy chips. >> >> Francois >> >> >> On 11/19/2009 10:56 PM, Sunny Srivastava wrote: >> >>> Dear Bioconductor Helpers, >>> I have used Bioconductor to analyze Affy chips only, but recently I have >>> to >>> do some analysis for Agilent array. Each array has the two chips with the >>> same sample but the dye swapped (I just made it clear as I saw most of >>> the >>> literature on such arrays with 4 chips). >>> >>> Can any one help me how to: >>> 1 - Import data in Bioconductor? (I mean what is the equivalent of .cel >>> files here - if there is any? I have a few .xml .csv, .txt and .shp files >>> - >>> I am clueless which ones to use and how should I use) >>> 2 - I saw two packages - AgiMicroRNA and Agi4x44PreProcess (the latter >>> seems >>> to be for the 4 chip Agilent array) related to Agilent arrays. >>> Can anyone point out a good article to read on - how to (completely) >>> analyze such Agilent Arrays - importing, "cleaning up" and analyzing >>> data? >>> 3 - I saw Limma talks about dye swap analysis, so I guess I can use Limma >>> to >>> analyze this data after I am done importing data correctly. >>> >>> I am sorry if I used Agilent array/chip in a wrong way, my knowledge is >>> very >>> limited in this area. I have only analyzed Affy arrays until now. >>> >>> Any help will be appreciated. >>> >>> Thanks, >>> S. >>> >>> [[alternative HTML version deleted]] >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor@stat.math.ethz.ch >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > [[alternative HTML version deleted]]
ADD REPLYlink written 9.9 years ago by Sunny Srivastava340
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 134 users visited in the last hour