looking for data file for ATH1 (GPL198)
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@matthew-mccall-4459
Last seen 2.4 years ago
United States
Ann, Unfortunately there isn't currently an fRMA implementation for ATH1. It is on the to-do list, but as you might imagine, that list is very long. You could create your own implementation using the frmaTools package described in: McCall MN* and Irizarry RA (2011). Thawing Frozen Robust Multi-array Analysis (fRMA), BMC Bioinformatics, 12:369. Best, Matt On Fri, Oct 4, 2013 at 12:32 PM, Loraine, Ann <ann.loraine at="" uncc.edu=""> wrote: > Hello, > > I would like to use fRMA to process data from the ATH1 (GPL198) microarray > from Affymetrix. > > Is there a data file I can use for that array ? e.g., something like > hgu133afrmavecs but for the GPL198/ATH1 platform? > > If yes, what is it called and how do I load it? > > Thank you and best wishes, > > Ann Loraine > > ------------------------------- > Ann Loraine, Ph.D. > Associate Professor > Department of Bioinformatics and Genomics > University of North Carolina at Charlotte > North Carolina Research Campus > 600 Laureate Way > Kannapolis, NC 28081 > 704-250-5750 > aloraine at uncc.edu > http://www.transvar.org > http://www.bioviz.org > http://www.uncc.edu > -- Matthew N McCall, PhD 112 Arvine Heights Rochester, NY 14611 Cell: 202-222-5880
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Loraine, Ann ▴ 50
@loraine-ann-5437
Last seen 7.2 years ago
Hello, I would like to use fRMA to process data from the ATH1 (GPL198) microarray from Affymetrix. Is there a data file I can use for that array – e.g., something like hgu133afrmavecs but for the GPL198/ATH1 platform? If yes, what is it called and how do I load it? Thank you and best wishes, Ann Loraine ------------------------------- Ann Loraine, Ph.D. Associate Professor Department of Bioinformatics and Genomics University of North Carolina at Charlotte North Carolina Research Campus 600 Laureate Way Kannapolis, NC 28081 704-250-5750 aloraine@uncc.edu http://www.transvar.org http://www.bioviz.org http://www.uncc.edu [[alternative HTML version deleted]]
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Loraine, Ann ▴ 50
@loraine-ann-5437
Last seen 7.2 years ago
Thank you for getting back to me so quickly. I will try to make an frma data file for the ATH1/GPL198 array using frmaTools. Follow-up question: Can you explain what is meant by this line in the frmaTools vignette? "Create batch ids based on your arrays." and then: vectors <- makeVectorsAffyBatch(files, batch.id) The help documentation says "batch.id" is a vector. I understand that I need to associate CEL file names with batches, but I don't understand how the structure of "batch.id" allows me to do this. What should "batch.id" contain and how do I relate it to "files" ? On 10/4/13 5:11 PM, "Matthew McCall" <mccallm at="" gmail.com=""> wrote: >Ann, > >Unfortunately there isn't currently an fRMA implementation for ATH1. >It is on the to-do list, but as you might imagine, that list is very >long. You could create your own implementation using the frmaTools >package described in: >McCall MN* and Irizarry RA (2011). Thawing Frozen Robust Multi-array >Analysis (fRMA), BMC Bioinformatics, 12:369. > >Best, >Matt > >On Fri, Oct 4, 2013 at 12:32 PM, Loraine, Ann <ann.loraine at="" uncc.edu=""> >wrote: >> Hello, >> >> I would like to use fRMA to process data from the ATH1 (GPL198) >>microarray >> from Affymetrix. >> >> Is there a data file I can use for that array ? e.g., something like >> hgu133afrmavecs but for the GPL198/ATH1 platform? >> >> If yes, what is it called and how do I load it? >> >> Thank you and best wishes, >> >> Ann Loraine >> >> ------------------------------- >> Ann Loraine, Ph.D. >> Associate Professor >> Department of Bioinformatics and Genomics >> University of North Carolina at Charlotte >> North Carolina Research Campus >> 600 Laureate Way >> Kannapolis, NC 28081 >> 704-250-5750 >> aloraine at uncc.edu >> http://www.transvar.org >> http://www.bioviz.org >> http://www.uncc.edu >> > > > >-- >Matthew N McCall, PhD >112 Arvine Heights >Rochester, NY 14611 >Cell: 202-222-5880
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