Question: New Bioconductor Package: SCAN.UPC
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gravatar for W. Evan Johnson
7.2 years ago by
United States
W. Evan Johnson800 wrote:
Hey Bioconductor Users, I just wanted to give you all a 'heads-up' on a new package (SCAN.UPC) that appeared in last week's release of Bioconductor. In the The SCAN normalization is a new single sample Affy normalization approach that only requires information within the sample, and does not need other samples or a set of reference samples for the normalization. The great thing about this is that it means that once you normalize the array once, the normalized values won't change if other arrays are added to the expression set. This has great utility in meta-analysis and in personalized medicine applications. The details of our SCAN method can be found here (http://www.sciencedirect.com/science/article/pii/S0888754312001632). SCAN removes background variation and increases the signal-to-noise ratio in the samples. We are seeing instances where batch effects are removed or reduced from batches of data as well. The method is a major and uniform upgrade over RMA, and is showing slightly better or equivalent results compared to fRMA. The advantage over fRMA is that you don't need to provide a frozen reference vector for the normalization--which is difficult for some arrays and applications. Also we are seeing improved performance when combining across Affy array platforms because fRMA will need different frozen vectors for the different array platforms. Please let us know if you have any issues with the package. We are happy to help! Evan
normalization affy frma • 577 views
ADD COMMENTlink modified 7.1 years ago by Stephen Piccolo560 • written 7.2 years ago by W. Evan Johnson800
Answer: New Bioconductor Package: SCAN.UPC
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gravatar for Stephen Piccolo
7.1 years ago by
United States
Stephen Piccolo560 wrote:
Hi Anthony, OK, sorry again for the delay. We now have a function called "UPC" in the SCAN.UPC package that will produce a probability that each gene/probeset is expressed above background. The parameters are identical to those for the SCAN function. This function is part of Bioconductor 2.12, which is the current developmental version and will be released in a few months. However, you are welcome to try it out now. You'll just need to install the development versions of R and Bioconductor. Please let me know if you have any questions. Regards, -Steve P.S. I've copied the Bioconductor list in case others have the same question. > >On 10/10/2011 Wed, Oct 10, 2011 9:59 PM, "Anthony Bosco" ><anthonyb at="" ichr.uwa.edu.au=""> wrote: > >>Dear Evan, >> >>I have just tried your SCAN preprocessing on some microarray data and >>the results look fantastic! >> >>In your paper you mention that SCAN estimates 79 % of the probes are >>measuring noise only and have no signal above background. >> >>Is it possible to flag these probes and remove them from downstream >>analysis? >> >>Best regards, >> >>Anthony >> >> >>-----Original Message----- >>From: bioconductor-bounces at r-project.org >>[mailto:bioconductor-bounces at r-project.org] On Behalf Of W. Evan >>Johnson >>Sent: Wednesday, 10 October 2012 8:27 PM >>To: bioconductor at r-project.org >>Cc: Andrea Bild; Steve Piccolo >>Subject: [BioC] New Bioconductor Package: SCAN.UPC >> >>Hey Bioconductor Users, >> >>I just wanted to give you all a 'heads-up' on a new package (SCAN.UPC) >>that appeared in last week's release of Bioconductor. In the The SCAN >>normalization is a new single sample Affy normalization approach that >>only requires information within the sample, and does not need other >>samples or a set of reference samples for the normalization. The great >>thing about this is that it means that once you normalize the array >>once, the normalized values won't change if other arrays are added to >>the expression set. This has great utility in meta-analysis and in >>personalized medicine applications. >> >>The details of our SCAN method can be found here >>(http://www.sciencedirect.com/science/article/pii/S0888754312001632) . >>SCAN removes background variation and increases the signal-to-noise >>ratio in the samples. We are seeing instances where batch effects are >>removed or reduced from batches of data as well. The method is a major >>and uniform upgrade over RMA, and is showing slightly better or >>equivalent results compared to fRMA. The advantage over fRMA is that >>you don't need to provide a frozen reference vector for the >>normalization--which is difficult for some arrays and applications. >>Also we are seeing improved performance when combining across Affy >>array platforms because fRMA will need different frozen vectors for the > >>different array platforms. >> >>Please let us know if you have any issues with the package. We are >>happy to help! >> >>Evan >>_______________________________________________ >>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 >> >>-- >>This message has been scanned for viruses and dangerous content by >>MailScanner, and is believed to be clean. >> > > >-- >This message has been scanned for viruses and dangerous content by >MailScanner, and is believed to be clean.
ADD COMMENTlink written 7.1 years ago by Stephen Piccolo560
On Fri, Oct 19, 2012 at 3:36 PM, Steve Piccolo <stephen.piccolo at="" hsc.utah.edu=""> wrote: [snip] > This function is part of Bioconductor 2.12, which is the current > developmental version and will be released in a few months. [/snip] Just F-anybody's-I (FAI), given that bioc 2.11 was just released: "in a few months" actually means "in 6 months" ... -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact
ADD REPLYlink written 7.1 years ago by Steve Lianoglou12k
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