Question: frma for Nimblegen arrays?
0
gravatar for wrighth
7.1 years ago by
wrighth260
wrighth260 wrote:
Quick (belated) followup question on this: is it possible to get oligo to summarize the probe-level expression rather than the gene level expression? We'd like to try to experiment with some of the other gene-level methods (such as the WGCNA collapseRows, for example) and just see how individual probes may be doing. I tried using the target="probeset" argument and that doesn't seem to work. Would I need to specify something when I set up the annotation object from the NDF? Hollis Wright, PhD Ojeda Lab, Division of Neuroscience Oregon Health and Science University ________________________________________ From: Benilton Carvalho [beniltoncarvalho@gmail.com] Sent: Tuesday, October 30, 2012 10:38 AM To: Hollis Wright Cc: bioconductor at r-project.org Subject: Re: [BioC] frma for Nimblegen arrays? The "generic XYS file" is meant to be actually one of your samples (any of them, its just to work as a template)... So, I'm confident you did everything right. b :) On 30 October 2012 16:58, Hollis Wright <wrighth at="" ohsu.edu=""> wrote: > Thanks, Benilton; I think I figured it out with buildPDInfoPkgs. However, just to be sure; we were provided an NDF file but I don't think we got a generic XYS file, so I used one of the actual array files for the XYS. It seemed to work alright, but could that be problematic? > > Hollis Wright, PhD > Ojeda Lab, Division of Neuroscience > Oregon Health and Science University > > ________________________________________ > From: Benilton Carvalho [beniltoncarvalho at gmail.com] > Sent: Tuesday, October 30, 2012 2:56 AM > To: Hollis Wright > Cc: bioconductor at r-project.org > Subject: Re: [BioC] frma for Nimblegen arrays? > > Hi Hollis, > > I'm the one who builds all the annotation packages for and I'm > positive that this annotation package was never provided through > BioC... I'm happy to help you out with that though. > > benilton > > On 29 October 2012 18:17, Hollis Wright <wrighth at="" ohsu.edu=""> wrote: >> Thanks, Matthew. As a followup, is there no longer an annotation package available for the rat arrays for oligo? I'm getting an error: >> >> biocLite("pd.100718.rat.hx12.expr") >> BioC_mirror: http://bioconductor.org >> Using Bioconductor version 2.11 (BiocInstaller 1.8.3), R version 2.15. >> Installing package(s) 'pd.100718.rat.hx12.expr' >> Warning messages: >> 1: package ?pd.100718.rat.hx12.expr? is not available (for R version 2.15.0) >> >> I searched the Bioconductor site and the package doesn't come up, and I can't seem to find anything with Google either. Is this just a version thing? >> >> Hollis Wright, PhD >> Ojeda Lab, Division of Neuroscience >> Oregon Health and Science University >> >> >> ________________________________________ >> From: Matthew McCall [mccallm at gmail.com] >> Sent: Monday, October 29, 2012 9:41 AM >> To: Hollis Wright >> Cc: bioconductor at r-project.org >> Subject: Re: [BioC] frma for Nimblegen arrays? >> >> Hollis, >> >> 1. I highly doubt that Nimblegen is using fRMA. >> >> 2. There isn't an fRMA implementation for Nimblegen arrays currently. >> You could in theory use a modified version of the code in the >> frmaTools package to make your own vectors, but it is probably better >> to just use RMA. >> >> Best, >> Matt >> >> On Mon, Oct 29, 2012 at 12:35 PM, Hollis Wright <wrighth at="" ohsu.edu=""> wrote: >>> Hello, all: two-part question here. We have some expression data from Nimblegen rat arrays that was normalized from our microarray service using the internal RMA process Nimblegen uses in their software. Unfortunately, a few of the arrays had physical defects. We've pulled those from our downstream analysis just to be safe but we're unsure if they were used in the normalization process. We've gone ahead with downstream analysis but I'd also like to make sure we're not running into any issues that were baked into the current normalization, just to be safe. So: >>> >>> 1) Should we be concerned in the first place about whether or not these arrays were included in the normalization process? I can't seem to find out exactly what flavor of RMA variant Nimblegen is using. If it's frma, since the normalizations are precomputed it shouldn't matter if the bad arrays were included, should it? >>> >>> 2) Assuming we should be concerned and renormalize, is this easily possible with frma? We have non-normalized data but we don't have the tiff files, just the calls/pairs/xys files. Is that sufficient? Sorry for the basic questions, I've not done microarray normalization in quite a while and that was all on an Affy platform. >>> >>> Thanks! >>> >>> Hollis Wright, PhD >>> Ojeda Lab, Division of Neuroscience >>> Oregon Health and Science University >>> _______________________________________________ >>> 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 >> >> >> >> -- >> Matthew N McCall, PhD >> 112 Arvine Heights >> Rochester, NY 14611 >> Cell: 202-222-5880 >> >> _______________________________________________ >> 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 COMMENTlink modified 7.1 years ago by Benilton Carvalho4.3k • written 7.1 years ago by wrighth260
Answer: frma for Nimblegen arrays?
0
gravatar for Benilton Carvalho
7.1 years ago by
Brazil/Campinas/UNICAMP
Benilton Carvalho4.3k wrote:
It sounds like that "summarize to the probe-level" is simply normalize the data (possibly after background correction) and not summarize at all? library(oligoData) data(nimbleExpressionFS) pns = probeNames(nimbleExpressionFS) sns = sampleNames(nimbleExpressionFS) pms = pm(nimbleExpressionFS) pms = backgroundCorrect(pms) pms = normalize(pms) colnames(pms) = sns rownames(pms) = pns head(pms) b On 10 November 2012 00:02, Hollis Wright <wrighth@ohsu.edu> wrote: > Quick (belated) followup question on this: is it possible to get oligo to > summarize the probe-level expression rather than the gene level expression? > We'd like to try to experiment with some of the other gene-level methods > (such as the WGCNA collapseRows, for example) and just see how individual > probes may be doing. I tried using the target="probeset" argument and that > doesn't seem to work. Would I need to specify something when I set up the > annotation object from the NDF? > > Hollis Wright, PhD > Ojeda Lab, Division of Neuroscience > Oregon Health and Science University > ________________________________________ > From: Benilton Carvalho [beniltoncarvalho@gmail.com] > Sent: Tuesday, October 30, 2012 10:38 AM > To: Hollis Wright > Cc: bioconductor@r-project.org > Subject: Re: [BioC] frma for Nimblegen arrays? > > The "generic XYS file" is meant to be actually one of your samples > (any of them, its just to work as a template)... So, I'm confident you > did everything right. b :) > > On 30 October 2012 16:58, Hollis Wright <wrighth@ohsu.edu> wrote: > > Thanks, Benilton; I think I figured it out with buildPDInfoPkgs. > However, just to be sure; we were provided an NDF file but I don't think we > got a generic XYS file, so I used one of the actual array files for the > XYS. It seemed to work alright, but could that be problematic? > > > > Hollis Wright, PhD > > Ojeda Lab, Division of Neuroscience > > Oregon Health and Science University > > > > ________________________________________ > > From: Benilton Carvalho [beniltoncarvalho@gmail.com] > > Sent: Tuesday, October 30, 2012 2:56 AM > > To: Hollis Wright > > Cc: bioconductor@r-project.org > > Subject: Re: [BioC] frma for Nimblegen arrays? > > > > Hi Hollis, > > > > I'm the one who builds all the annotation packages for and I'm > > positive that this annotation package was never provided through > > BioC... I'm happy to help you out with that though. > > > > benilton > > > > On 29 October 2012 18:17, Hollis Wright <wrighth@ohsu.edu> wrote: > >> Thanks, Matthew. As a followup, is there no longer an annotation > package available for the rat arrays for oligo? I'm getting an error: > >> > >> biocLite("pd.100718.rat.hx12.expr") > >> BioC_mirror: http://bioconductor.org > >> Using Bioconductor version 2.11 (BiocInstaller 1.8.3), R version 2.15. > >> Installing package(s) 'pd.100718.rat.hx12.expr' > >> Warning messages: > >> 1: package ‘pd.100718.rat.hx12.expr’ is not available (for R version > 2.15.0) > >> > >> I searched the Bioconductor site and the package doesn't come up, and I > can't seem to find anything with Google either. Is this just a version > thing? > >> > >> Hollis Wright, PhD > >> Ojeda Lab, Division of Neuroscience > >> Oregon Health and Science University > >> > >> > >> ________________________________________ > >> From: Matthew McCall [mccallm@gmail.com] > >> Sent: Monday, October 29, 2012 9:41 AM > >> To: Hollis Wright > >> Cc: bioconductor@r-project.org > >> Subject: Re: [BioC] frma for Nimblegen arrays? > >> > >> Hollis, > >> > >> 1. I highly doubt that Nimblegen is using fRMA. > >> > >> 2. There isn't an fRMA implementation for Nimblegen arrays currently. > >> You could in theory use a modified version of the code in the > >> frmaTools package to make your own vectors, but it is probably better > >> to just use RMA. > >> > >> Best, > >> Matt > >> > >> On Mon, Oct 29, 2012 at 12:35 PM, Hollis Wright <wrighth@ohsu.edu> > wrote: > >>> Hello, all: two-part question here. We have some expression data from > Nimblegen rat arrays that was normalized from our microarray service using > the internal RMA process Nimblegen uses in their software. Unfortunately, a > few of the arrays had physical defects. We've pulled those from our > downstream analysis just to be safe but we're unsure if they were used in > the normalization process. We've gone ahead with downstream analysis but > I'd also like to make sure we're not running into any issues that were > baked into the current normalization, just to be safe. So: > >>> > >>> 1) Should we be concerned in the first place about whether or not > these arrays were included in the normalization process? I can't seem to > find out exactly what flavor of RMA variant Nimblegen is using. If it's > frma, since the normalizations are precomputed it shouldn't matter if the > bad arrays were included, should it? > >>> > >>> 2) Assuming we should be concerned and renormalize, is this easily > possible with frma? We have non-normalized data but we don't have the tiff > files, just the calls/pairs/xys files. Is that sufficient? Sorry for the > basic questions, I've not done microarray normalization in quite a while > and that was all on an Affy platform. > >>> > >>> Thanks! > >>> > >>> Hollis Wright, PhD > >>> Ojeda Lab, Division of Neuroscience > >>> Oregon Health and Science University > >>> _______________________________________________ > >>> 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 > >> > >> > >> > >> -- > >> Matthew N McCall, PhD > >> 112 Arvine Heights > >> Rochester, NY 14611 > >> Cell: 202-222-5880 > >> > >> _______________________________________________ > >> 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 > > _______________________________________________ > 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 7.1 years ago by Benilton Carvalho4.3k
This still seems to be giving me a gene/transcript level summary, however: > pns = probeNames(rat_files_400) > sns = sampleNames(rat_files_400) > pms = pm(rat_files_400) > pms = backgroundCorrect(pms) Background correcting... OK > pms = normalize(pms) Normalizing... OK > colnames(pms) = sns > rownames(pms) = pns > head(pms) 544146A03_SO043_LP_Rep5_400_532.xys 544146A04_SO043_EJ_Rep6_400_532.xys NM_001024356 86.54111 30.76186 NM_001012351 7485.24882 8881.24834 XM_237393 38.09388 95.22230 XM_344019 197.06084 394.76741 NM_001008834 1659.76215 2765.05263 NM_001037655 218.92524 452.86810 ... To be clear as to what I'm going for, I'd like to see the expression for each of the five probesets per transcript rather than the summary of the five across the transcript. I'm using the custom library file for these arrays (pd.100718.rat.hx12.expr) that I built with the buildPDInfoPkg package to define the probe names, so I'm wondering if there's something I need to do at that level to get the individual probesets separated out vs. this summarization? Hollis Wright, PhD Ojeda Lab, Division of Neuroscience Oregon Health and Science University ________________________________________ From: Benilton Carvalho [beniltoncarvalho@gmail.com] Sent: Monday, November 12, 2012 3:17 AM To: Hollis Wright Cc: bioconductor at r-project.org Subject: Re: [BioC] frma for Nimblegen arrays? It sounds like that "summarize to the probe-level" is simply normalize the data (possibly after background correction) and not summarize at all? library(oligoData) data(nimbleExpressionFS) pns = probeNames(nimbleExpressionFS) sns = sampleNames(nimbleExpressionFS) pms = pm(nimbleExpressionFS) pms = backgroundCorrect(pms) pms = normalize(pms) colnames(pms) = sns rownames(pms) = pns head(pms) b On 10 November 2012 00:02, Hollis Wright <wrighth at="" ohsu.edu<mailto:wrighth="" at="" ohsu.edu="">> wrote: Quick (belated) followup question on this: is it possible to get oligo to summarize the probe-level expression rather than the gene level expression? We'd like to try to experiment with some of the other gene-level methods (such as the WGCNA collapseRows, for example) and just see how individual probes may be doing. I tried using the target="probeset" argument and that doesn't seem to work. Would I need to specify something when I set up the annotation object from the NDF? Hollis Wright, PhD Ojeda Lab, Division of Neuroscience Oregon Health and Science University ________________________________________ From: Benilton Carvalho [beniltoncarvalho@gmail.com<mailto:beniltoncarvalho@gmail.com>] Sent: Tuesday, October 30, 2012 10:38 AM To: Hollis Wright Cc: bioconductor at r-project.org<mailto:bioconductor at="" r-project.org=""> Subject: Re: [BioC] frma for Nimblegen arrays? The "generic XYS file" is meant to be actually one of your samples (any of them, its just to work as a template)... So, I'm confident you did everything right. b :) On 30 October 2012 16:58, Hollis Wright <wrighth at="" ohsu.edu<mailto:wrighth="" at="" ohsu.edu="">> wrote: > Thanks, Benilton; I think I figured it out with buildPDInfoPkgs. However, just to be sure; we were provided an NDF file but I don't think we got a generic XYS file, so I used one of the actual array files for the XYS. It seemed to work alright, but could that be problematic? > > Hollis Wright, PhD > Ojeda Lab, Division of Neuroscience > Oregon Health and Science University > > ________________________________________ > From: Benilton Carvalho [beniltoncarvalho at gmail.com<mailto:beniltoncarvalho at="" gmail.com="">] > Sent: Tuesday, October 30, 2012 2:56 AM > To: Hollis Wright > Cc: bioconductor at r-project.org<mailto:bioconductor at="" r-project.org=""> > Subject: Re: [BioC] frma for Nimblegen arrays? > > Hi Hollis, > > I'm the one who builds all the annotation packages for and I'm > positive that this annotation package was never provided through > BioC... I'm happy to help you out with that though. > > benilton > > On 29 October 2012 18:17, Hollis Wright <wrighth at="" ohsu.edu<mailto:wrighth="" at="" ohsu.edu="">> wrote: >> Thanks, Matthew. As a followup, is there no longer an annotation package available for the rat arrays for oligo? I'm getting an error: >> >> biocLite("pd.100718.rat.hx12.expr") >> BioC_mirror: http://bioconductor.org >> Using Bioconductor version 2.11 (BiocInstaller 1.8.3), R version 2.15. >> Installing package(s) 'pd.100718.rat.hx12.expr' >> Warning messages: >> 1: package ?pd.100718.rat.hx12.expr? is not available (for R version 2.15.0) >> >> I searched the Bioconductor site and the package doesn't come up, and I can't seem to find anything with Google either. Is this just a version thing? >> >> Hollis Wright, PhD >> Ojeda Lab, Division of Neuroscience >> Oregon Health and Science University >> >> >> ________________________________________ >> From: Matthew McCall [mccallm at gmail.com<mailto:mccallm at="" gmail.com="">] >> Sent: Monday, October 29, 2012 9:41 AM >> To: Hollis Wright >> Cc: bioconductor at r-project.org<mailto:bioconductor at="" r-project.org=""> >> Subject: Re: [BioC] frma for Nimblegen arrays? >> >> Hollis, >> >> 1. I highly doubt that Nimblegen is using fRMA. >> >> 2. There isn't an fRMA implementation for Nimblegen arrays currently. >> You could in theory use a modified version of the code in the >> frmaTools package to make your own vectors, but it is probably better >> to just use RMA. >> >> Best, >> Matt >> >> On Mon, Oct 29, 2012 at 12:35 PM, Hollis Wright <wrighth at="" ohsu.edu<mailto:wrighth="" at="" ohsu.edu="">> wrote: >>> Hello, all: two-part question here. We have some expression data from Nimblegen rat arrays that was normalized from our microarray service using the internal RMA process Nimblegen uses in their software. Unfortunately, a few of the arrays had physical defects. We've pulled those from our downstream analysis just to be safe but we're unsure if they were used in the normalization process. We've gone ahead with downstream analysis but I'd also like to make sure we're not running into any issues that were baked into the current normalization, just to be safe. So: >>> >>> 1) Should we be concerned in the first place about whether or not these arrays were included in the normalization process? I can't seem to find out exactly what flavor of RMA variant Nimblegen is using. If it's frma, since the normalizations are precomputed it shouldn't matter if the bad arrays were included, should it? >>> >>> 2) Assuming we should be concerned and renormalize, is this easily possible with frma? We have non-normalized data but we don't have the tiff files, just the calls/pairs/xys files. Is that sufficient? Sorry for the basic questions, I've not done microarray normalization in quite a while and that was all on an Affy platform. >>> >>> Thanks! >>> >>> Hollis Wright, PhD >>> Ojeda Lab, Division of Neuroscience >>> Oregon Health and Science University >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at r-project.org<mailto:bioconductor at="" r-project.org=""> >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> >> >> -- >> Matthew N McCall, PhD >> 112 Arvine Heights >> Rochester, NY 14611 >> Cell: 202-222-5880<tel:202-222-5880> >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org<mailto: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<mailto: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 7.1 years ago by wrighth260
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