Question: [XPS] integrating data processed outside of XPS into the tree
0
gravatar for thomas sierocinski
8.2 years ago by
thomas sierocinski50 wrote:
Dear All, Dear Christian, I'm using XPS to process/analyse human Exon arrays. I would like to use fRMA (frozen Robust MultiArray Analysis) to normalize/summarize the data. I'd like to know if is there a way to summarize/normalize data using fRMA in XPS. More generally, is there a way to process the data by other methods (non supported by XPS) and then use it in the XPS framework? Cheers, Thomas [[alternative HTML version deleted]]
process xps frma • 592 views
ADD COMMENTlink modified 8.2 years ago by cstrato3.9k • written 8.2 years ago by thomas sierocinski50
Answer: [XPS] integrating data processed outside of XPS into the tree
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gravatar for cstrato
8.2 years ago by
cstrato3.9k
Austria
cstrato3.9k wrote:
Dear Thomas, I was looking at the source code of fRMA, which currently supports only "hgu133a", "hgu133plus2", "mouse4302" arrays, and realized that it is not possible for me to support fRMA, since it depends on pre- calculated public-domain data which you need, e.g. hgu133afrmavecs. For this reason I cannot support fRMA. However, keep in mind that fRMA still uses RMA as algorithm. Best regards Christian On 9/24/11 1:32 AM, thomas sierocinski wrote: > Dear All, Dear Christian, > > I'm using XPS to process/analyse human Exon arrays. > I would like to use fRMA (frozen Robust MultiArray Analysis) to > normalize/summarize the data. > I'd like to know if is there a way to summarize/normalize data using > fRMA in XPS. > More generally, is there a way to process the data by other methods (non > supported by XPS) and then use it in the XPS framework? > > Cheers, > > Thomas > > >
ADD COMMENTlink written 8.2 years ago by cstrato3.9k
Dear Chrisitan, Thanks for your answer. Is there any way to assign a data matrix (created outside XPS) to a ROOT tree? Cheers, Thomas 2011/9/24 cstrato <cstrato@aon.at> > Dear Thomas, > > I was looking at the source code of fRMA, which currently supports only > "hgu133a", "hgu133plus2", "mouse4302" arrays, and realized that it is not > possible for me to support fRMA, since it depends on pre-calculated > public-domain data which you need, e.g. hgu133afrmavecs. For this reason I > cannot support fRMA. However, keep in mind that fRMA still uses RMA as > algorithm. > > Best regards > Christian > > > > On 9/24/11 1:32 AM, thomas sierocinski wrote: > >> Dear All, Dear Christian, >> >> I'm using XPS to process/analyse human Exon arrays. >> I would like to use fRMA (frozen Robust MultiArray Analysis) to >> normalize/summarize the data. >> I'd like to know if is there a way to summarize/normalize data using >> fRMA in XPS. >> More generally, is there a way to process the data by other methods (non >> supported by XPS) and then use it in the XPS framework? >> >> Cheers, >> >> Thomas >> >> >> >> [[alternative HTML version deleted]]
ADD REPLYlink written 8.2 years ago by thomas sierocinski50
Dear Thomas, Yes, it is possible, see the examples in the help files ?'intensity<-' and ?'expr<-'. ad 1, intensity<- You can create new raw data, e.g. a user of xps has once applied "vsn" to the raw data and then imported the result into DataTreeSet using 'intensity<-'. However, be careful since CEL-files will be created, see the help file. ad 2, expr<- In principle it is possible to import any result of preprocessing into an ExprTreeSet. For example you could use fRMA and then import the result using 'expr<-'. I hope that this is the information you are looking for, however it would be helpful if you could explain in more detail what you would like to do. Best regards Christian On 9/27/11 10:04 PM, thomas sierocinski wrote: > Dear Chrisitan, > > Thanks for your answer. > > Is there any way to assign a data matrix (created outside XPS) to a ROOT > tree? > > Cheers, > > Thomas > > 2011/9/24 cstrato <cstrato at="" aon.at="" <mailto:cstrato="" at="" aon.at="">> > > Dear Thomas, > > I was looking at the source code of fRMA, which currently supports > only "hgu133a", "hgu133plus2", "mouse4302" arrays, and realized that > it is not possible for me to support fRMA, since it depends on > pre-calculated public-domain data which you need, e.g. > hgu133afrmavecs. For this reason I cannot support fRMA. However, > keep in mind that fRMA still uses RMA as algorithm. > > Best regards > Christian > > > > On 9/24/11 1:32 AM, thomas sierocinski wrote: > > Dear All, Dear Christian, > > I'm using XPS to process/analyse human Exon arrays. > I would like to use fRMA (frozen Robust MultiArray Analysis) to > normalize/summarize the data. > I'd like to know if is there a way to summarize/normalize data using > fRMA in XPS. > More generally, is there a way to process the data by other > methods (non > supported by XPS) and then use it in the XPS framework? > > Cheers, > > Thomas > > > >
ADD REPLYlink written 8.2 years ago by cstrato3.9k
This is very helpful. Thanks. Thomas 2011/9/27 cstrato <cstrato@aon.at> > Dear Thomas, > > Yes, it is possible, see the examples in the help files ?'intensity<-' and > ?'expr<-'. > > ad 1, intensity<- > You can create new raw data, e.g. a user of xps has once applied "vsn" to > the raw data and then imported the result into DataTreeSet using > 'intensity<-'. However, be careful since CEL-files will be created, see the > help file. > > ad 2, expr<- > In principle it is possible to import any result of preprocessing into an > ExprTreeSet. For example you could use fRMA and then import the result using > 'expr<-'. > > I hope that this is the information you are looking for, however it would > be helpful if you could explain in more detail what you would like to do. > > Best regards > Christian > > > > On 9/27/11 10:04 PM, thomas sierocinski wrote: > >> Dear Chrisitan, >> >> Thanks for your answer. >> >> Is there any way to assign a data matrix (created outside XPS) to a ROOT >> tree? >> >> Cheers, >> >> Thomas >> >> 2011/9/24 cstrato <cstrato@aon.at <mailto:cstrato@aon.at="">> >> >> >> Dear Thomas, >> >> I was looking at the source code of fRMA, which currently supports >> only "hgu133a", "hgu133plus2", "mouse4302" arrays, and realized that >> it is not possible for me to support fRMA, since it depends on >> pre-calculated public-domain data which you need, e.g. >> hgu133afrmavecs. For this reason I cannot support fRMA. However, >> keep in mind that fRMA still uses RMA as algorithm. >> >> Best regards >> Christian >> >> >> >> On 9/24/11 1:32 AM, thomas sierocinski wrote: >> >> Dear All, Dear Christian, >> >> I'm using XPS to process/analyse human Exon arrays. >> I would like to use fRMA (frozen Robust MultiArray Analysis) to >> normalize/summarize the data. >> I'd like to know if is there a way to summarize/normalize data >> using >> fRMA in XPS. >> More generally, is there a way to process the data by other >> methods (non >> supported by XPS) and then use it in the XPS framework? >> >> Cheers, >> >> Thomas >> >> >> >> >> -- ----------------------------------------------------------- Thomas Sierocinski, PhD Genomic Analyst GenomeDx Biosciences Inc. | 201-1595 W. 3rd Ave Vancouver, BC V6J 1J8 | Canada *Phone: 604-569-0072 | Fax: 866-505-5161* email: *thomas@genomedx.com* http://www.genomedx.com ------------------------------------------------------------ This email and any attachments to it may be confidential and are intended solely for the use of the individual to whom it is addressed. If you are not the intended recipient of this email, you must neither take any action based upon its contents, nor copy or show it to anyone. Please contact the sender if you believe you have received this email in error thank you. [[alternative HTML version deleted]]
ADD REPLYlink written 8.2 years ago by thomas sierocinski50
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