Question: frma for Nimblegen arrays?
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gravatar for wrighth
7.1 years ago by
wrighth260
wrighth260 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
ADD COMMENTlink modified 7.1 years ago by Matthew McCall830 • written 7.1 years ago by wrighth260
Answer: frma for Nimblegen arrays?
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gravatar for Matthew McCall
7.1 years ago by
United States
Matthew McCall830 wrote:
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
ADD COMMENTlink written 7.1 years ago by Matthew McCall830
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 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
ADD REPLYlink written 7.1 years ago by wrighth260
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 REPLYlink written 7.1 years ago by Benilton Carvalho4.3k
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 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 REPLYlink written 7.1 years ago by wrighth260
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 REPLYlink written 7.1 years ago by Benilton Carvalho4.3k
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