Question: normalization one color microarrays
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gravatar for Paz Tapia Ramirez
8.1 years ago by
Paz Tapia Ramirez150 wrote:
Hello, I am starting to work with ONE color microarrays from Agilent, and I read that during the pre-processing is main tasks, such as background adjustment, normalization and summarization. Currently I have corrected the background and normalized samples, but do not understand the step of the summarization. Can you help me please? Thks, Paz [[alternative HTML version deleted]]
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ADD COMMENTlink modified 8.1 years ago by Freudenberg, Johannes NIH/NIEHS [E]150 • written 8.1 years ago by Paz Tapia Ramirez150
Answer: normalization one color microarrays
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gravatar for Paz Tapia Ramirez
8.1 years ago by
Paz Tapia Ramirez40 wrote:
Hello, I am starting to work with ONE color microarrays from Agilent, and I read that during the pre-processing is main tasks, such as background adjustment, normalization and summarization. Currently I have corrected the background and normalized samples, but do not understand the step of the summarization. Can you help me please? Thks, Paz [[alternative HTML version deleted]]
ADD COMMENTlink written 8.1 years ago by Paz Tapia Ramirez40
Answer: normalization one color microarrays
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gravatar for Sean Davis
8.1 years ago by
Sean Davis21k
United States
Sean Davis21k wrote:
On Wed, Aug 24, 2011 at 4:08 PM, Paz Tapia Ramirez <verotapia at="" alumnos.utalca.cl=""> wrote: > > > > > > > > > > Hello, I am starting to work with ONE color microarrays from Agilent, and I read that during the pre-processing is main tasks, such as background adjustment, normalization and summarization. Currently I have corrected the background and ?normalized samples, but do not understand the step of the summarization. Can you help me please? > Hi, Paz. For Agilent, there is not typically a summarization step (pulling multiple probes into a "probe set"). Each probe is designed to measure nucleotides independently. Sean
ADD COMMENTlink written 8.1 years ago by Sean Davis21k
On 2011-08-24 23:04, Sean Davis wrote: > On Wed, Aug 24, 2011 at 4:08 PM, Paz Tapia Ramirez > <verotapia at="" alumnos.utalca.cl=""> wrote: >> >> >> >> >> >> >> >> >> Hello, I am starting to work with ONE color microarrays from Agilent, and I read that during the pre-processing is main tasks, such as background adjustment, normalization and summarization. Currently I have corrected the background and normalized samples, but do not understand the step of the summarization. Can you help me please? >> > Hi, Paz. > > For Agilent, there is not typically a summarization step (pulling > multiple probes into a "probe set"). Each probe is designed to > measure nucleotides independently. > > Sean > This depends on the use case, and what is typical to a lab might to an other. For custom arrays, I have seen a lot of designs with several probes per genes and there a probe summarization step could be applied. L. > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD REPLYlink written 8.1 years ago by Laurent Gautier2.2k
On Wed, Aug 24, 2011 at 5:12 PM, Laurent Gautier <laurent at="" cbs.dtu.dk=""> wrote: > On 2011-08-24 23:04, Sean Davis wrote: >> >> On Wed, Aug 24, 2011 at 4:08 PM, Paz Tapia Ramirez >> <verotapia at="" alumnos.utalca.cl=""> ?wrote: >>> >>> >>> >>> >>> >>> >>> >>> >>> Hello, I am starting to work with ONE color microarrays from Agilent, and >>> I read that during the pre-processing is main tasks, such as background >>> adjustment, normalization and summarization. Currently I have corrected the >>> background and ?normalized samples, but do not understand the step of the >>> summarization. Can you help me please? >>> >> Hi, Paz. >> >> For Agilent, there is not typically a summarization step (pulling >> multiple probes into a "probe set"). ?Each probe is designed to >> measure nucleotides independently. >> >> Sean >> > > This depends on the use case, and what is typical to a lab might to an > other. > For custom arrays, I have seen a lot of designs with several probes per > genes and there a probe summarization step could be applied. Good point. Sean >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >
ADD REPLYlink written 8.1 years ago by Sean Davis21k
Answer: normalization one color microarrays
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gravatar for Freudenberg, Johannes NIH/NIEHS [E]
8.1 years ago by
Hi Paz, I was able to run the code that you sent me without any trouble. However, here is the output I get: FILTERING BY ControlType FLAG ------------------------------------------------------ PROBES BEFORE FILTERING: 12015 PROBES AFTER ControlType FILTERING: 11259 RAW DATA WITHOUT CONTROLS OUT : 11259 ------------------------------------------------------ Are you sure you have the right annotation package? It looks like you might be trying to process some other array (one that has 45,220 "probes before filtering" rather than 12,015) with the same annotation package "hgug4112a.db". Other packages are available here: http://www.bioconductor.org/packages/2.8/data/annotation/ --Johannes From: Paz Tapia Ramirez [mailto:verotapia@alumnos.utalca.cl] Sent: Monday, August 29, 2011 1:26 PM To: Freudenberg, Johannes (NIH/NIEHS) [E] Subject: RE: [BioC] normalization one color microarrays Step 14 is: ################################################### ### chunk number 14: filter.probes ################################################### ddFILT=filter.probes(ddNORM, control=TRUE, wellaboveBG=TRUE, isfound=TRUE, wellaboveNEG=TRUE, sat=TRUE, PopnOL=TRUE, NonUnifOL=T, nas=TRUE, limWellAbove=75, limISF=75, limNEG=75, limSAT=75, limPopnOL=75, limNonUnifOL=75, limNAS=100, makePLOT=F,annotation.package="hgug4112a.db",flag.counts=T,targets) I can run the step 13 (Correction background and Normalization). sessionInfo() says: R version 2.11.1 (2010-05-31) i686-pc-linux-gnu locale: [1] LC_CTYPE=es_ES.utf8 LC_NUMERIC=C [3] LC_TIME=es_ES.utf8 LC_COLLATE=es_ES.utf8 [5] LC_MONETARY=C LC_MESSAGES=es_ES.utf8 [7] LC_PAPER=es_ES.utf8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=es_ES.utf8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] vsn_3.16.0 annotate_1.26.1 hgug4112a.db_2.4.1 [4] org.Hs.eg.db_2.4.1 RSQLite_0.9-4 DBI_0.2-5 [7] AnnotationDbi_1.10.2 Biobase_2.8.0 marray_1.26.0 [10] limma_3.4.5 loaded via a namespace (and not attached): [1] affy_1.26.1 affyio_1.16.0 grid_2.11.1 [4] lattice_0.19-26 preprocessCore_1.10.0 xtable_1.5-6 and specifically in step 14 says: FILTERING BY ControlType FLAG ------------------------------------------------------ PROBES BEFORE FILTERING: 45220 PROBES AFTER ControlType FILTERING: 0 RAW DATA WITHOUT CONTROLS OUT : 0 ------------------------------------------------------ FILTERING BY IsWellAboveBG filterFLAG FLAG FILTERING OPTIONS - FLAG OK = 1 - limWellAbove: 75 % PROBES BEFORE FILTERING: 0 PROBES AFTER QC FILTERING: 0 IsNOTWellAboveBG OUT : 0 ------------------------------------------------------ FILTERING BY gIsFound filterFLAG FLAG FILTERING OPTIONS - FLAG OK = 1 - limISF: 75 % PROBES AFTER gIsFound FILTERING: 0 IsNOTFound OUT : 0 ------------------------------------------------------ Error en if (aux[jj] >= Limit[pos[jj]]) { : valor ausente donde TRUE/FALSE es necesario Thanks, Paz ________________________________ From: johannes.freudenberg@nih.gov<mailto:johannes.freudenberg@nih.gov> To: verotapia@alumnos.utalca.cl<mailto:verotapia@alumnos.utalca.cl> CC: bioconductor@stat.math.ethz.ch<mailto:bioconductor@stat.math.ethz.ch> Date: Mon, 29 Aug 2011 13:12:42 -0400 Subject: RE: [BioC] normalization one color microarrays Can you please be more specific? I'm not really sure what step 14 is. What exactly doesn't work? Please provide an example that doesn't work for you and the kind of error messages it produces. It's also a good idea to provide the output of > sessionInfo() when you post a question like this to the list. --Johannes From: Paz Tapia Ramirez [mailto:verotapia@alumnos.utalca.cl]<mailto:[m ailto:verotapia@alumnos.utalca.cl]=""> Sent: Monday, August 29, 2011 1:06 PM To: Freudenberg, Johannes (NIH/NIEHS) [E] Cc: bioconductor@stat.math.ethz.ch<mailto:bioconductor@stat.math.ethz.ch> Subject: RE: [BioC] normalization one color microarrays when I work with Agi4x44PreProcess, from step 14 onwards it does not work ________________________________ From: johannes.freudenberg@nih.gov<mailto:johannes.freudenberg@nih.gov> To: verotapia@alumnos.utalca.cl<mailto:verotapia@alumnos.utalca.cl> CC: bioconductor@stat.math.ethz.ch<mailto:bioconductor@stat.math.ethz.ch> Date: Mon, 29 Aug 2011 13:01:46 -0400 Subject: RE: [BioC] normalization one color microarrays Hi Paz, I'm not exactly sure what kind of microarrays you are trying to process but I'm guessing you are talking about Agilent 4x44 gene expression arrays. If that is the case, I would recommend to use the Agi4x44Preprocess package. You can download this package here: http://www.bioconductor.org/packages/2.3/bioc/html/Agi4x44PreProcess.h tml or by running the following in R > source("http://bioconductor.org/biocLite.R") > biocLite("Agi4x44PreProcess") This package comes with a nice manual which explains all the steps. It also has plenty of examples you can try. You can find the manual here: http://www.bioconductor.org/packages/2.3/bioc/vignettes/Agi4x44PreProc ess/inst/doc/Agi4x44PreProcess.pdf I hope this helps for now. Let me know if you more specific questions. --Johannes From: Paz Tapia Ramirez [mailto:verotapia@alumnos.utalca.cl]<mailto:[m ailto:verotapia@alumnos.utalca.cl]=""> Sent: Monday, August 29, 2011 12:25 PM To: Freudenberg, Johannes (NIH/NIEHS) [E]; bioconductor@stat.math.ethz.ch<mailto:bioconductor@stat.math.ethz.ch>; bioconductor-bounces@r-project.org<mailto:bioconductor- bounces@r-project.org=""> Subject: RE: [BioC] normalization one color microarrays Hi, but if I make not summarization process, how do I build the set of expression? > From: johannes.freudenberg@nih.gov<mailto:johannes.freudenberg@nih.gov> > To: verotapia@alumnos.utalca.cl<mailto:verotapia@alumnos.utalca.cl> > Date: Wed, 24 Aug 2011 16:17:07 -0400 > Subject: RE: [BioC] normalization one color microarrays > > Summarization really only applies to Affymetrix arrays where you have several probes per probeset. > > --Johannes > > > -----Original Message----- > From: Paz Tapia Ramirez [mailto:verotapia@alumnos.utalca.cl]<mailto: [mailto:verotapia@alumnos.utalca.cl]=""> > Sent: Wednesday, August 24, 2011 4:09 PM > To: bioconductor@stat.math.ethz.ch<mailto:bioconductor@stat.math.ethz.ch>; bioconductor-bounces@r-project.org<mailto:bioconductor- bounces@r-project.org=""> > Subject: [BioC] normalization one color microarrays > > > > > > > > > > > Hello, I am starting to work with ONE color microarrays from Agilent, and I read that during the pre-processing is main tasks, such as background adjustment, normalization and summarization. Currently I have corrected the background and normalized samples, but do not understand the step of the summarization. Can you help me please? > > Thks, > Paz > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org<mailto:bioconductor@r-project.org> > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor [[alternative HTML version deleted]]
ADD COMMENTlink written 8.1 years ago by Freudenberg, Johannes NIH/NIEHS [E]150
Answer: normalization one color microarrays
0
gravatar for Paz Tapia Ramirez
8.1 years ago by
Paz Tapia Ramirez150 wrote:
Hi, but if I make not summarization process, how do I build the set of expression? > From: johannes.freudenberg@nih.gov > To: verotapia@alumnos.utalca.cl > Date: Wed, 24 Aug 2011 16:17:07 -0400 > Subject: RE: [BioC] normalization one color microarrays > > Summarization really only applies to Affymetrix arrays where you have several probes per probeset. > > --Johannes > > > -----Original Message----- > From: Paz Tapia Ramirez [mailto:verotapia@alumnos.utalca.cl] > Sent: Wednesday, August 24, 2011 4:09 PM > To: bioconductor@stat.math.ethz.ch; bioconductor- bounces@r-project.org > Subject: [BioC] normalization one color microarrays > > > > > > > > > > > Hello, I am starting to work with ONE color microarrays from Agilent, and I read that during the pre-processing is main tasks, such as background adjustment, normalization and summarization. Currently I have corrected the background and normalized samples, but do not understand the step of the summarization. Can you help me please? > > Thks, > Paz > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor [[alternative HTML version deleted]]
ADD COMMENTlink written 8.1 years ago by Paz Tapia Ramirez150
Hi Paz, I'm not exactly sure what kind of microarrays you are trying to process but I'm guessing you are talking about Agilent 4x44 gene expression arrays. If that is the case, I would recommend to use the Agi4x44Preprocess package. You can download this package here: http://www.bioconductor.org/packages/2.3/bioc/html/Agi4x44PreProcess.h tml or by running the following in R > source("http://bioconductor.org/biocLite.R") > biocLite("Agi4x44PreProcess") This package comes with a nice manual which explains all the steps. It also has plenty of examples you can try. You can find the manual here: http://www.bioconductor.org/packages/2.3/bioc/vignettes/Agi4x44PreProc ess/inst/doc/Agi4x44PreProcess.pdf I hope this helps for now. Let me know if you more specific questions. --Johannes From: Paz Tapia Ramirez [mailto:verotapia@alumnos.utalca.cl] Sent: Monday, August 29, 2011 12:25 PM To: Freudenberg, Johannes (NIH/NIEHS) [E]; bioconductor@stat.math.ethz.ch; bioconductor-bounces@r-project.org Subject: RE: [BioC] normalization one color microarrays Hi, but if I make not summarization process, how do I build the set of expression? > From: johannes.freudenberg@nih.gov<mailto:johannes.freudenberg@nih.gov> > To: verotapia@alumnos.utalca.cl<mailto:verotapia@alumnos.utalca.cl> > Date: Wed, 24 Aug 2011 16:17:07 -0400 > Subject: RE: [BioC] normalization one color microarrays > > Summarization really only applies to Affymetrix arrays where you have several probes per probeset. > > --Johannes > > > -----Original Message----- > From: Paz Tapia Ramirez [mailto:verotapia@alumnos.utalca.cl]<mailto: [mailto:verotapia@alumnos.utalca.cl]=""> > Sent: Wednesday, August 24, 2011 4:09 PM > To: bioconductor@stat.math.ethz.ch<mailto:bioconductor@stat.math.ethz.ch>; bioconductor-bounces@r-project.org<mailto:bioconductor- bounces@r-project.org=""> > Subject: [BioC] normalization one color microarrays > > > > > > > > > > > Hello, I am starting to work with ONE color microarrays from Agilent, and I read that during the pre-processing is main tasks, such as background adjustment, normalization and summarization. Currently I have corrected the background and normalized samples, but do not understand the step of the summarization. Can you help me please? > > Thks, > Paz > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org<mailto:bioconductor@r-project.org> > 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 8.1 years ago by Freudenberg, Johannes NIH/NIEHS [E]150
Answer: normalization one color microarrays
0
gravatar for Paz Tapia Ramirez
8.1 years ago by
Paz Tapia Ramirez150 wrote:
when I work with Agi4x44PreProcess, from step 14 onwards it does not work From: johannes.freudenberg@nih.gov To: verotapia@alumnos.utalca.cl CC: bioconductor@stat.math.ethz.ch Date: Mon, 29 Aug 2011 13:01:46 -0400 Subject: RE: [BioC] normalization one color microarrays Hi Paz, I’m not exactly sure what kind of microarrays you are trying to process but I’m guessing you are talking about Agilent 4x44 gene expression arrays. If that is the case, I would recommend to use the Agi4x44Preprocess package. You can download this package here: http: //www.bioconductor.org/packages/2.3/bioc/html/Agi4x44PreProcess.html or by running the following in R > source("http://bioconductor.org/biocLite.R")> biocLite("Agi4x44PreProcess") This package comes with a nice manual which explains all the steps. It also has plenty of examples you can try. You can find the manual here: http://www.bioconductor.org/packag es/2.3/bioc/vignettes/Agi4x44PreProcess/inst/doc/Agi4x44PreProcess.pdf I hope this helps for now. Let me know if you more specific questions. --Johannes From: Paz Tapia Ramirez [mailto:verotapia@alumnos.utalca.cl] Sent: Monday, August 29, 2011 12:25 PM To: Freudenberg, Johannes (NIH/NIEHS) [E]; bioconductor@stat.math.ethz.ch; bioconductor-bounces@r-project.org Subject: RE: [BioC] normalization one color microarrays Hi, but if I make not summarization process, how do I build the set of expression?> From: johannes.freudenberg@nih.gov > To: verotapia@alumnos.utalca.cl > Date: Wed, 24 Aug 2011 16:17:07 -0400 > Subject: RE: [BioC] normalization one color microarrays > > Summarization really only applies to Affymetrix arrays where you have several probes per probeset. > > --Johannes > > > -----Original Message----- > From: Paz Tapia Ramirez [mailto:verotapia@alumnos.utalca.cl] > Sent: Wednesday, August 24, 2011 4:09 PM > To: bioconductor@stat.math.ethz.ch; bioconductor- bounces@r-project.org > Subject: [BioC] normalization one color microarrays > > > > > > > > > > > Hello, I am starting to work with ONE color microarrays from Agilent, and I read that during the pre-processing is main tasks, such as background adjustment, normalization and summarization. Currently I have corrected the background and normalized samples, but do not understand the step of the summarization. Can you help me please? > > Thks, > Paz > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor [[alternative HTML version deleted]]
ADD COMMENTlink written 8.1 years ago by Paz Tapia Ramirez150
Can you please be more specific? I'm not really sure what step 14 is. What exactly doesn't work? Please provide an example that doesn't work for you and the kind of error messages it produces. It's also a good idea to provide the output of > sessionInfo() when you post a question like this to the list. --Johannes From: Paz Tapia Ramirez [mailto:verotapia@alumnos.utalca.cl] Sent: Monday, August 29, 2011 1:06 PM To: Freudenberg, Johannes (NIH/NIEHS) [E] Cc: bioconductor@stat.math.ethz.ch Subject: RE: [BioC] normalization one color microarrays when I work with Agi4x44PreProcess, from step 14 onwards it does not work ________________________________ From: johannes.freudenberg@nih.gov<mailto:johannes.freudenberg@nih.gov> To: verotapia@alumnos.utalca.cl<mailto:verotapia@alumnos.utalca.cl> CC: bioconductor@stat.math.ethz.ch<mailto:bioconductor@stat.math.ethz.ch> Date: Mon, 29 Aug 2011 13:01:46 -0400 Subject: RE: [BioC] normalization one color microarrays Hi Paz, I'm not exactly sure what kind of microarrays you are trying to process but I'm guessing you are talking about Agilent 4x44 gene expression arrays. If that is the case, I would recommend to use the Agi4x44Preprocess package. You can download this package here: http://www.bioconductor.org/packages/2.3/bioc/html/Agi4x44PreProcess.h tml or by running the following in R > source("http://bioconductor.org/biocLite.R") > biocLite("Agi4x44PreProcess") This package comes with a nice manual which explains all the steps. It also has plenty of examples you can try. You can find the manual here: http://www.bioconductor.org/packages/2.3/bioc/vignettes/Agi4x44PreProc ess/inst/doc/Agi4x44PreProcess.pdf I hope this helps for now. Let me know if you more specific questions. --Johannes From: Paz Tapia Ramirez [mailto:verotapia@alumnos.utalca.cl]<mailto:[m ailto:verotapia@alumnos.utalca.cl]=""> Sent: Monday, August 29, 2011 12:25 PM To: Freudenberg, Johannes (NIH/NIEHS) [E]; bioconductor@stat.math.ethz.ch<mailto:bioconductor@stat.math.ethz.ch>; bioconductor-bounces@r-project.org<mailto:bioconductor- bounces@r-project.org=""> Subject: RE: [BioC] normalization one color microarrays Hi, but if I make not summarization process, how do I build the set of expression? > From: johannes.freudenberg@nih.gov<mailto:johannes.freudenberg@nih.gov> > To: verotapia@alumnos.utalca.cl<mailto:verotapia@alumnos.utalca.cl> > Date: Wed, 24 Aug 2011 16:17:07 -0400 > Subject: RE: [BioC] normalization one color microarrays > > Summarization really only applies to Affymetrix arrays where you have several probes per probeset. > > --Johannes > > > -----Original Message----- > From: Paz Tapia Ramirez [mailto:verotapia@alumnos.utalca.cl]<mailto: [mailto:verotapia@alumnos.utalca.cl]=""> > Sent: Wednesday, August 24, 2011 4:09 PM > To: bioconductor@stat.math.ethz.ch<mailto:bioconductor@stat.math.ethz.ch>; bioconductor-bounces@r-project.org<mailto:bioconductor- bounces@r-project.org=""> > Subject: [BioC] normalization one color microarrays > > > > > > > > > > > Hello, I am starting to work with ONE color microarrays from Agilent, and I read that during the pre-processing is main tasks, such as background adjustment, normalization and summarization. Currently I have corrected the background and normalized samples, but do not understand the step of the summarization. Can you help me please? > > Thks, > Paz > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org<mailto:bioconductor@r-project.org> > 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 8.1 years ago by Freudenberg, Johannes NIH/NIEHS [E]150
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