background correction with cDNA array data
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@qizhangastrazenecacom-105
Last seen 10.2 years ago
Dear all, I have searched through the bioconductor ducument and this mailing list, but could not find a general guidance about how to correct background in cDNA array data. I have imported my data (GPR files from GenePix) using functions from marray. Now what are the available methods for background correction before normalization? Any suggestions/experience is very much appreciated. Regards, Qi Zhang
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Naomi Altman ★ 6.0k
@naomi-altman-380
Last seen 3.6 years ago
United States
Did you want to write your own background correction method? The normalization routines in marray and limma do background correction. --Naomi At 04:51 PM 10/26/2005, Qi.Zhang at astrazeneca.com wrote: >Dear all, > >I have searched through the bioconductor ducument and this mailing list, but >could not find a general guidance about how to correct background in cDNA >array data. I have imported my data (GPR files from GenePix) using >functions from marray. Now what are the available methods for background >correction before normalization? Any suggestions/experience is very much >appreciated. > >Regards, > >Qi Zhang > >_______________________________________________ >Bioconductor mailing list >Bioconductor at stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor Naomi S. Altman 814-865-3791 (voice) Associate Professor Dept. of Statistics 814-863-7114 (fax) Penn State University 814-865-1348 (Statistics) University Park, PA 16802-2111
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@qizhangastrazenecacom-105
Last seen 10.2 years ago
Naomi, thanks for your reply. I do not intent to write my own mathod. I took the default option when read in the gpr file using read.GenePix, so I assume the background correction was done by "substraction". I remember it from somewhere that the "substraction" may introduce additional variance depends on the algorithm of the background estimation (from the iamge analysis software). Is the "substraction" the only bg correction method in marray? limma has more options, but I have no idea about the advantage or disadvantage of them. Any suggestions will be very helpful. Thanks. Qi -----Original Message----- From: Naomi Altman [mailto:naomi@stat.psu.edu] Sent: Wednesday, October 26, 2005 7:42 PM To: Zhang, Qi; bioconductor at stat.math.ethz.ch Subject: Re: [BioC] background correction with cDNA array data Did you want to write your own background correction method? The normalization routines in marray and limma do background correction. --Naomi At 04:51 PM 10/26/2005, Qi.Zhang at astrazeneca.com wrote: >Dear all, > >I have searched through the bioconductor ducument and this mailing list, but >could not find a general guidance about how to correct background in cDNA >array data. I have imported my data (GPR files from GenePix) using >functions from marray. Now what are the available methods for background >correction before normalization? Any suggestions/experience is very much >appreciated. > >Regards, > >Qi Zhang > >_______________________________________________ >Bioconductor mailing list >Bioconductor at stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor Naomi S. Altman 814-865-3791 (voice) Associate Professor Dept. of Statistics 814-863-7114 (fax) Penn State University 814-865-1348 (Statistics) University Park, PA 16802-2111
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You can also have a look at the recent book: "Bioinformatics and Computational Biology Solutions Using R and Bioconductor" from Robert Gentleman, Vince Carey, Wolfgang Huber, Rafael Irizarry and Sandrine Dudoit. http://www.bioconductor.org/pub/docs/mogr/ They have done a great job. David On Oct 27, 2005, at 5:01, Qi.Zhang at astrazeneca.com wrote: > Naomi, thanks for your reply. I do not intent to write my own mathod. > I > took the default option when read in the gpr file using read.GenePix, > so I > assume the background correction was done by "substraction". I > remember it > from somewhere that the "substraction" may introduce additional > variance > depends on the algorithm of the background estimation (from the iamge > analysis software). Is the "substraction" the only bg correction > method in > marray? limma has more options, but I have no idea about the > advantage or > disadvantage of them. Any suggestions will be very helpful. > > Thanks. > > Qi > > -----Original Message----- > From: Naomi Altman [mailto:naomi at stat.psu.edu] > Sent: Wednesday, October 26, 2005 7:42 PM > To: Zhang, Qi; bioconductor at stat.math.ethz.ch > Subject: Re: [BioC] background correction with cDNA array data > > > Did you want to write your own background correction method? The > normalization routines in marray and limma do background correction. > > --Naomi > > At 04:51 PM 10/26/2005, Qi.Zhang at astrazeneca.com wrote: >> Dear all, >> >> I have searched through the bioconductor ducument and this mailing >> list, > but >> could not find a general guidance about how to correct background in >> cDNA >> array data. I have imported my data (GPR files from GenePix) using >> functions from marray. Now what are the available methods for >> background >> correction before normalization? Any suggestions/experience is very >> much >> appreciated. >> >> Regards, >> >> Qi Zhang >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor > > Naomi S. Altman 814-865-3791 (voice) > Associate Professor > Dept. of Statistics 814-863-7114 (fax) > Penn State University 814-865-1348 (Statistics) > University Park, PA 16802-2111 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >
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@qizhangastrazenecacom-105
Last seen 10.2 years ago
Naomi, thanks for your reply. I do not intent to write my own mathod. I took the default option when read in the gpr file using read.GenePix, so I assume the background correction was done by "substraction". I remember it from somewhere that the "substraction" may introduce additional variance depends on the algorithm of the background estimation (from the iamge analysis software). Is the "substraction" the only bg correction method in marray? limma has more options, but I have no idea about the advantage or disadvantage of them. Any suggestions will be very helpful. Thanks. Qi -----Original Message----- From: Naomi Altman [mailto:naomi@stat.psu.edu] Sent: Wednesday, October 26, 2005 7:42 PM To: Zhang, Qi; bioconductor at stat.math.ethz.ch Subject: Re: [BioC] background correction with cDNA array data Did you want to write your own background correction method? The normalization routines in marray and limma do background correction. --Naomi At 04:51 PM 10/26/2005, Qi.Zhang at astrazeneca.com wrote: >Dear all, > >I have searched through the bioconductor ducument and this mailing list, but >could not find a general guidance about how to correct background in cDNA >array data. I have imported my data (GPR files from GenePix) using >functions from marray. Now what are the available methods for background >correction before normalization? Any suggestions/experience is very much >appreciated. > >Regards, > >Qi Zhang > >_______________________________________________ >Bioconductor mailing list >Bioconductor at stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor Naomi S. Altman 814-865-3791 (voice) Associate Professor Dept. of Statistics 814-863-7114 (fax) Penn State University 814-865-1348 (Statistics) University Park, PA 16802-2111
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@sean-davis-490
Last seen 12 weeks ago
United States
On 10/26/05 11:01 PM, "Qi.Zhang at astrazeneca.com" <qi.zhang at="" astrazeneca.com=""> wrote: > Naomi, thanks for your reply. I do not intent to write my own mathod. I > took the default option when read in the gpr file using read.GenePix, so I > assume the background correction was done by "substraction". I remember it > from somewhere that the "substraction" may introduce additional variance > depends on the algorithm of the background estimation (from the iamge > analysis software). Is the "substraction" the only bg correction method in > marray? limma has more options, but I have no idea about the advantage or > disadvantage of them. Any suggestions will be very helpful. All the bioconductor packages contain extensive help, and limma has some of the best help files available. Simply reading the help for the backgroundCorrect function in limma gives you a rather concise description of the various options available. There are also references given which you can certainly pull for more information. If contemplating using limma, a required read is the relevant section(s) of the limma user guide. All that said, there is nothing wrong with trying each method and then plotting your data to get a feel for what is really going on with your data. Sean
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@giuseppepalermoboinfnit-1475
Last seen 10.2 years ago
I'm not sure if this can help you. I also was interested in methods for background subtraction, and most of all in understanding if or not subtract the background. The only paper I found about last topic is: "When should one subtract background fluorescence in two color microarrays", by Parmigianini at. al. Give a look, may be can help you. Regards Giuseppe Quoting Qi.Zhang at astrazeneca.com: > Dear all, > > I have searched through the bioconductor ducument and this mailing list, but > could not find a general guidance about how to correct background in cDNA > array data. I have imported my data (GPR files from GenePix) using > functions from marray. Now what are the available methods for background > correction before normalization? Any suggestions/experience is very much > appreciated. > > Regards, > > Qi Zhang > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >

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