Question: rma on new samples
0
gravatar for Malick.PAYE@eu.biomerieux.com
12.6 years ago by
An embedded and charset-unspecified text was scrubbed... Name: not available Url: https://stat.ethz.ch/pipermail/bioconductor/attachments/20070305/ 8fee777a/attachment.pl
• 326 views
ADD COMMENTlink modified 12.6 years ago by Kuhn, Max70 • written 12.6 years ago by Malick.PAYE@eu.biomerieux.com110
Answer: rma on new samples
0
gravatar for Hassane, Duane
12.6 years ago by
Hassane, Duane110 wrote:
Malick, A few months back, Chris Harbron posted a reply to a related question in which the RefPlus package was suggested for this purpose. Best, Duane _________________________________________________ Duane Hassane, Ph.D. Center for Pediatric Biomedical Research University of Rochester Medical Center Rochester, New York 14642 -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch]On Behalf Of Malick.PAYE at eu.biomerieux.com Sent: Monday, March 05, 2007 1:47 PM To: bioconductor at stat.math.ethz.ch Subject: [BioC] rma on new samples hello, I work for an invitro diagnostic company www.biomerieux.com) and we are interested in classification of patients based on expression profile (we are working with affymetrix chips). I built a classification model based on a training set and i have new samples and i want to make my new samples comparable with the training set in order to apply my built model. We use RMA to compute expression measures. If someone have a code to do this, it would be very greatful for me. Ideally i want to extract rma parameters and apply them to my new samples, or if someone have a better idea. Thanks in advance. M.P Malick Paye | bioM?rieux | Biomathematician Phone: (+33)4 78 87 70 97 | Fax: (+33)4 78 87 53 40 [Centre Cristophe M?rieux, 5 Rue des Berges, 38004 Cedex 01 Grenoble, France] ---------------------------------------------------------------------- ------- AVIS : Ce courrier et ses pieces jointes sont destines a leur seul destinataire et peuvent contenir des informations confidentielles appartenant a bioMerieux. Si vous n'etes pas destinataire, vous etes informe que toute lecture, divulgation, ou reproduction de ce message et des pieces jointes est strictement interdite. Si vous avez recu ce message par erreur merci d'en prevenir l'expediteur et de le detruire, ainsi que ses pieces jointes. NOTICE: This message and attachments are intended only for the use of their addressee and may contain confidential information belonging to bioMerieux. If you are not the intended recipient, you are hereby notified that any reading, dissemination, distribution, or copying of this message, or any attachment, is strictly prohibited. If you have received this message in error, please notify the original sender immediately and delete this message, along with any attachments. [[alternative HTML version deleted]]
ADD COMMENTlink written 12.6 years ago by Hassane, Duane110
Answer: rma on new samples
0
gravatar for Kuhn, Max
12.6 years ago by
Kuhn, Max70
Kuhn, Max70 wrote:
There are a few ways to do this. The basic issue is that the RMA normalization and summarization steps use data across multiple chips. There is a package called refRMA that normalizes to a pre-defined database of data generated by GeneLogic. See http://www.biomedcentral.com/content/pdf/1471-2105-7-464.pdf for more details. I have approached the problem by keeping the background correction the same and then - normalize the PM values of new samples to a reference distribution defined by the training set PM values - computing a trimmed mean to get the summary measure I'm sure that others have done something similar too. I have code to do this (the normalization is based on some code from limma:::normalizeQuantiles). I will send you (or anyone else) the code in another email if you are interested. I've looked at comparisons in performance in my approach, regular RMA and MAS5 and found that the two RMA methods are pretty similar and MAS5 did very poorly. This could have been due to my particular problem and data (I was using the Staph chip), so take that for what it's worth. Max -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor- bounces@stat.math.ethz.ch] On Behalf Of Malick.PAYE@eu.biomerieux.com Sent: Monday, March 05, 2007 1:47 PM To: bioconductor at stat.math.ethz.ch Subject: [BioC] rma on new samples hello, I work for an invitro diagnostic company www.biomerieux.com) and we are interested in classification of patients based on expression profile (we are working with affymetrix chips). I built a classification model based on a training set and i have new samples and i want to make my new samples comparable with the training set in order to apply my built model. We use RMA to compute expression measures. If someone have a code to do this, it would be very greatful for me. Ideally i want to extract rma parameters and apply them to my new samples, or if someone have a better idea. Thanks in advance. M.P Malick Paye | bioM?rieux | Biomathematician Phone: (+33)4 78 87 70 97 | Fax: (+33)4 78 87 53 40 [Centre Cristophe M?rieux, 5 Rue des Berges, 38004 Cedex 01 Grenoble, France] ---------------------------------------------------------------------- ------- AVIS : Ce courrier et ses pieces jointes sont destines a leur seul destinataire et peuvent contenir des informations confidentielles appartenant a bioMerieux. Si vous n'etes pas destinataire, vous etes informe que toute lecture, divulgation, ou reproduction de ce message et des pieces jointes est strictement interdite. Si vous avez recu ce message par erreur merci d'en prevenir l'expediteur et de le detruire, ainsi que ses pieces jointes. NOTICE: This message and attachments are intended only for the use of their addressee and may contain confidential information belonging to bioMerieux. If you are not the intended recipient, you are hereby notified that any reading, dissemination, distribution, or copying of this message, or any attachment, is strictly prohibited. If you have received this message in error, please notify the original sender immediately and delete this message, along with any attachments. [[alternative HTML version deleted]] ---------------------------------------------------------------------- LEGAL NOTICE\ Unless expressly stated otherwise, this messag...{{dropped}}
ADD COMMENTlink written 12.6 years ago by Kuhn, Max70
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 323 users visited in the last hour