External expression data/ MAS5 Signal

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Sek Won Kong, M.D. ▴ 40

@sek-won-kong-md-42

Last seen 10.2 years ago

This is a multi-part message in MIME format. ------=_NextPart_000_008E_01C212C8.50292C70 Content-Type: text/plain; charset="ks_c_5601-1987" Content-Transfer-Encoding: 7bit Dear all two quick questions #1. how can I import the external expression value table to affy? If possible, in which format? #2. I saw AvgDiff, AvgDiff2, rma, and li.wong in express. Is it possible to calculate the Signal value which is implemented to Microarray Suite version 5 in affy? Thank you very much for the helps in advance. SW ------=_NextPart_000_008E_01C212C8.50292C70 Content-Type: text/html; charset="ks_c_5601-1987" Content-Transfer-Encoding: quoted-printable <html><head> <meta http-equiv="3DContent-Type" content="3D"text/html;" =="" charset="3Dks_c_5601-1987""> <meta content="3D"MSHTML" 6.00.2716.2200"="" name="3DGENERATOR"> <style></style> </head> <body bgcolor="3D#ffffff">

Dear all

two quick questions

#1. how can I import the external = expression value=20 table to affy? If possible, in which format?

#2. I saw AvgDiff, AvgDiff2, rma, and = li.wong in=20 express. Is it possible to calculate the Signal value which is = implemented to=20 Microarray Suite version 5 in affy?

Thank you very much for the helps in=20 advance.

SW

</body></html> ------=_NextPart_000_008E_01C212C8.50292C70--

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ADD COMMENT • link updated 22.4 years ago by Isaac Neuhaus ▴ 360 • written 22.5 years ago by Sek Won Kong, M.D. ▴ 40

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Rafael A. Irizarry ▴ 640

@rafael-a-irizarry-14

Last seen 10.2 years ago

> #1. how can I import the external expression value table to affy? If > possible, in which format? what do you mean by external expression value table? if its just a flat file you can use read.table (an R command) > #2. I saw AvgDiff, AvgDiff2, rma, and li.wong in express. Is it possible to > calculate the Signal value which is implemented to Microarray Suite version > 5 in affy? > as far as i know the algorithm isnt public yet so we can't incorporate it. > Thank you very much for the helps in advance. > > SW >

ADD COMMENT • link 22.5 years ago Rafael A. Irizarry ▴ 640

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On Thu, 2002-06-13 at 09:59, Rafael A. Irizarry wrote: > > #1. how can I import the external expression value table to affy? If > > possible, in which format? > what do you mean by external expression value table? if its just a flat > file you can use read.table (an R command) > > > #2. I saw AvgDiff, AvgDiff2, rma, and li.wong in express. Is it possible to > > calculate the Signal value which is implemented to Microarray Suite version > > 5 in affy? > > > as far as i know the algorithm isnt public yet so we can't incorporate it. Can I propose a little change in express, that will accomodate background specific correction as in the case of MAS5. Specifically, parameter bg that is used to specify the background adjustment function, expects only functions that work on a chip or probe pair level, but not on a probeset level, such as MAS5. The thing is when the data comes to summary.stat, which is a function working on the probe level, the probe pairs are already reduced to single number and it is too late to apply MAS5. For more info look at http://www.stat.berkeley.edu/users/terry/zarray/Affy/affy_index.html So, one way to fix this is to have the factor levels used to split the (globally) adjusted pm's, to be passed as a parameter to bg()(and bgc() in version 1.1.0), and every other function that doesn't use them, to use "...". Thanks, Peter > > > > Thank you very much for the helps in advance. > > > > SW > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor

ADD REPLY • link 22.5 years ago Peter Dimitrov ▴ 30

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On Thu, Jun 13, 2002 at 10:34:46AM -0700, Peter Dimitrov wrote: > On Thu, 2002-06-13 at 09:59, Rafael A. Irizarry wrote: > > > #1. how can I import the external expression value table to affy? If > > > possible, in which format? > > what do you mean by external expression value table? if its just a flat > > file you can use read.table (an R command) > > > > > #2. I saw AvgDiff, AvgDiff2, rma, and li.wong in express. Is it possible to > > > calculate the Signal value which is implemented to Microarray Suite version > > > 5 in affy? > > > > > as far as i know the algorithm isnt public yet so we can't incorporate it. > > Can I propose a little change in express, that will accomodate > background specific correction as in the case of MAS5. Specifically, > parameter bg that is used to specify the background adjustment function, > expects only functions that work on a chip or probe pair level, but not > on a probeset level, such as MAS5. The thing is when the data comes to > summary.stat, which is a function working on the probe level, the probe > pairs are already reduced to single number and it is too late to apply > MAS5. For more info look at > http://www.stat.berkeley.edu/users/terry/zarray/Affy/affy_index.html Dear Peter, One can do what you describe using the method generateExprSet (for objects of class Cel.container) of the version 1.1.x of the package (in the devel section)... your comments are welcome if you have a chance to look at it... regards, L. -- -------------------------------------------------------------- Laurent Gautier CBS, Building 208, DTU PhD. Student DK-2800 Lyngby,Denmark tel: +45 45 25 24 85 http://www.cbs.dtu.dk/laurent

ADD REPLY • link 22.5 years ago Laurent Gautier ★ 2.3k

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Laurent Gautier ★ 2.3k

@laurent-gautier-29

Last seen 10.2 years ago

On Thu, Jun 13, 2002 at 02:04:50PM -0400, Sek Won Kong, M.D. wrote: (...) > > I wondered there's quite a difference in calculated expression values from > AvgDiff, AvgDiff2, li.wong and rma. Previous I used invariant set normalized > MAS 5 signal values for analysis. However when I tried to implement the > quantile normalization and rma, there's big differences in reults ( I mean > the final results the list of genes ). So I wondered the why, and wanted to > compare 5 different kinds of expression algorithms. The 'because' that answers the 'why' is probably linked with the fact that the methods are fairly different (see their respective description in the help pages)... You may want to look at the individual probe sets for the genes for which the results are very different. (try the function get.PPset)... do not hesitate to give us feedback about the differences observed. > > And could you let me know how to calculate the PM-only model of Li- Wong in > affy? li.wong seems like PM-MM model. > In the package, we consider that PMs and MMs probe intensities are used to compute 'adjusted' probe intensities. In the case of PMs-MMs, it can be thought of subtracting the noise to the signal. The parameter 'bg' for express or 'bg.correct' for generateExprSet (for Plob and Cel.container respectively) let you specify how to get the 'adjusted' values. The function 'bg.correct.pmonly' returns only the PMs and can be used... regards, Laurent -- -------------------------------------------------------------- Laurent Gautier CBS, Building 208, DTU PhD. Student DK-2800 Lyngby,Denmark tel: +45 45 25 24 85 http://www.cbs.dtu.dk/laurent

ADD COMMENT • link 22.5 years ago Laurent Gautier ★ 2.3k

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also keep in mind that rma return log2(expression). if you want to make a direct comp you should look at 2^exprs(express(Plob)) rma and li and dchip with no pm only give similar results. i think the average correlation is about .9 (on the log scale). for mas 5.0 its around .8. On Mon, 17 Jun 2002, Laurent Gautier wrote: > On Thu, Jun 13, 2002 at 02:04:50PM -0400, Sek Won Kong, M.D. wrote: > (...) > > > > I wondered there's quite a difference in calculated expression values from > > AvgDiff, AvgDiff2, li.wong and rma. Previous I used invariant set normalized > > MAS 5 signal values for analysis. However when I tried to implement the > > quantile normalization and rma, there's big differences in reults ( I mean > > the final results the list of genes ). So I wondered the why, and wanted to > > compare 5 different kinds of expression algorithms. > > The 'because' that answers the 'why' is probably linked with the fact that > the methods are fairly different (see their respective description in the > help pages)... > You may want to look at the individual probe sets for the genes for which > the results are very different. (try the function get.PPset)... do not > hesitate to give us feedback about the differences observed. > > > > > And could you let me know how to calculate the PM-only model of Li-Wong in > > affy? li.wong seems like PM-MM model. > > > > In the package, we consider that PMs and MMs probe intensities are used > to compute 'adjusted' probe intensities. In the case of PMs-MMs, > it can be thought of subtracting the noise to the signal. > > The parameter 'bg' for express or 'bg.correct' for generateExprSet > (for Plob and Cel.container respectively) let you specify how to > get the 'adjusted' values. > The function 'bg.correct.pmonly' returns only the PMs and can be > used... > > > regards, > > > Laurent > > > >

ADD REPLY • link 22.5 years ago Rafael A. Irizarry ▴ 640

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Sek Won Kong, M.D. ▴ 40

@sek-won-kong-md-42

Last seen 10.2 years ago

Dear Laurent i used log transformed and untransformed for both algorithms. and you are right, the r square is good enough for those algorithms. however, the small difference made quite a diffrerence when trying sam, samroc procedure for choosing the significant genes. that's the problem. usually 50-60% genes were found significant in both rma, li.wong, and MAS 5 with given same threshold or highest 500 rank genes. thanks! SW ----- Original Message ----- From: "Rafael A. Irizarry" <ririzarr@jhsph.edu> To: "Laurent Gautier" <> Cc: "Sek Won Kong, M.D." <skong@caregroup.harvard.edu>; <> Sent: Monday, June 17, 2002 9:31 AM Subject: Re: [BioC] External expression data/ MAS5 Signal > also keep in mind that rma return log2(expression). if you want to make > a direct comp you should look at 2^exprs(express(Plob)) > > rma and li and dchip with no pm only give similar results. i think the > average correlation is about .9 (on the log scale). for mas 5.0 its around .8. > > On > Mon, 17 Jun 2002, Laurent Gautier wrote: > > > On Thu, Jun 13, 2002 at 02:04:50PM -0400, Sek Won Kong, M.D. wrote: > > (...) > > > > > > I wondered there's quite a difference in calculated expression values from > > > AvgDiff, AvgDiff2, li.wong and rma. Previous I used invariant set normalized > > > MAS 5 signal values for analysis. However when I tried to implement the > > > quantile normalization and rma, there's big differences in reults ( I mean > > > the final results the list of genes ). So I wondered the why, and wanted to > > > compare 5 different kinds of expression algorithms. > > > > The 'because' that answers the 'why' is probably linked with the fact that > > the methods are fairly different (see their respective description in the > > help pages)... > > You may want to look at the individual probe sets for the genes for which > > the results are very different. (try the function get.PPset)... do not > > hesitate to give us feedback about the differences observed. > > > > > > > > And could you let me know how to calculate the PM-only model of Li-Wong in > > > affy? li.wong seems like PM-MM model. > > > > > > > In the package, we consider that PMs and MMs probe intensities are used > > to compute 'adjusted' probe intensities. In the case of PMs-MMs, > > it can be thought of subtracting the noise to the signal. > > > > The parameter 'bg' for express or 'bg.correct' for generateExprSet > > (for Plob and Cel.container respectively) let you specify how to > > get the 'adjusted' values. > > The function 'bg.correct.pmonly' returns only the PMs and can be > > used... > > > > > > regards, > > > > > > Laurent > > > > > > > >

ADD COMMENT • link 22.5 years ago Sek Won Kong, M.D. ▴ 40

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Laurent Gautier ★ 2.3k

@laurent-gautier-29

Last seen 10.2 years ago

On Fri, Jun 14, 2002 at 02:08:24PM -0700, Peter Dimitrov wrote: > Dear Laurant, > > Thanks for the suggestion, it seems good place to plug MAS5. But before > that, all of my data has to be transfered from Plobs to Cel.containers. > What is the easiest way to convert Plob object to Cel.container? I've > looked in the documentation, but still can't find an example of that, if > there is any. ...if you did not subset your Plob objects, it should be technically possible... feel free to contribute a converter Plob->Cel.container... (yep, it looks like there is no such converter in the package otherwise) The other way is to load your data (again) through function like 'read.container.celfile' and do your data processing over these objects. > > Regards, > > Peter > > P.S. There seems to be a bug in affy.subset(version 1.1.1). > Specifically, the assigment of pData slot of the phenotypic object ph > fails, because the subsetting operation of the data frame fails to > return a data.frame(is this an R bug?): 'can't say, 'had no time to look at it... (Rafael, Ben, Leslie, any idea ?) > > ... > ph <- phenoData(x) > if (!is.null(pData(ph)) || length(chips) < nchips(x)) > ph@pData <- pData(ph)[chips, ] > ... > > is.data.frame(pData(ph)[chips, ]) returns False and ph@pData is a data > frame. > > I choose to replace the asignment with this line: > > pData(ph) <- subset( pData(ph), rownames(pData(ph)) == chips ) > > assuming chips already is a list of chip names and not numeric indices. > There are other solutions also. > > Regards, Laurent -- -------------------------------------------------------------- Laurent Gautier CBS, Building 208, DTU PhD. Student DK-2800 Lyngby,Denmark tel: +45 45 25 24 85 http://www.cbs.dtu.dk/laurent

ADD COMMENT • link 22.5 years ago Laurent Gautier ★ 2.3k

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Isaac Neuhaus ▴ 360

@isaac-neuhaus-22

Last seen 9.5 years ago

United States

Affymetrix has fully described the MAS5.0 algorithm and they put it on the web. Here is the url: http://www.affymetrix.com/support/technical/whitepapers.affx Go to the bottom of the page and look for: Statistical Algorithms Description Document (pdf, 660 KB) Isaac "Rafael A. Irizarry" wrote: > > #1. how can I import the external expression value table to affy? If > > possible, in which format? > what do you mean by external expression value table? if its just a flat > file you can use read.table (an R command) > > > #2. I saw AvgDiff, AvgDiff2, rma, and li.wong in express. Is it possible to > > calculate the Signal value which is implemented to Microarray Suite version > > 5 in affy? > > > as far as i know the algorithm isnt public yet so we can't incorporate it. > > > Thank you very much for the helps in advance. > > > > SW > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor

ADD COMMENT • link 22.4 years ago Isaac Neuhaus ▴ 360

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