Hello, we use one-color Agilent chips (4x44 whole human genome) and I try to calculate the intensities like GeneSpring does. The problem is, that my values are a little bit different and i don't know why. First I read in the data from the Agilent-Files "gProcessedSignal". Some genes are nor unique, so I take the mean value for these gene intensities. Like GeneSpring I first divide each raw intensity value by the median of the chip and then divide each value by te median of each gene. Now I have the normalized values and I use the log2 function to recieve similar values to the GeneSpring values, but here is a little variation and the only thing I hav found, what GeneSpring does is the "median shift to percentile of 75". How can I perform this median shift to percentile? Maybe this is the key to find the correct values? Thanks in advance for any help! Martin ----------------------------------------- This email was sent from ATLAS Biolabs GmbH, Koeln/Cologne & Berlin. Sitz der Gesellschaft/Registered Office: Koeln/Cologne, Germany. Registergericht/Commercial Register Koeln/Cologne No HRB 59119, USt- IdNr: DE251633620 Diese E-Mail kann Betriebs- oder Geschaeftsgeheimnisse oder sonstige vertrauliche Informationen enthalten. Sollten Sie diese E-Mail irrtuemlich erhalten haben, ist Ihnen eine Kenntnisnahme des Inhalts, eine Vervielfaeltigung oder Weitergabe der E-Mail ausdruecklich untersagt. Bitte benachrichtigen Sie uns und vernichten Sie die empfangene E-Mail. Vielen Dank. This e-mail may contain trade secrets or privileged, undisclosed, or otherwise confidential information. If you have received this e-mail in error, you are hereby notified that any review, copying, or distribution of it is strictly prohibited. Please inform us immediately and destroy the original transmittal. Thank you for your cooperation.

Hi Martin, in my experience comparing GeneSpring to R/Bioc values, even for a simple RMA produces slight differences. Just what GeneSpring actually does to the data is a bit of a black box. Perhaps a question to the genespring users group (genespringusers at yahoogroups.com ) might yield a better answer. I'd also suggest using log2 before taking all of the normalizations to medians, since this might account for some small differences. i'm not familiar with the "median shift to percentile of 75", so perhaps someone else can help with that. cheers, Mark On 16/06/2008, at 6:48 PM, olszewski at atlas-biolabs.de wrote: > Hello, > > we use one-color Agilent chips (4x44 whole human genome) and I try to > calculate the intensities like GeneSpring does. The problem is, that > my > values are a little bit different and i don't know why. > > First I read in the data from the Agilent-Files "gProcessedSignal". > Some genes are nor unique, so I take the mean value for these gene > intensities. > Like GeneSpring I first divide each raw intensity value by the > median of > the chip and then divide each value by te median of each gene. > Now I have the normalized values and I use the log2 function to > recieve > similar values to the GeneSpring values, but here is a little > variation > and the only thing I hav found, what GeneSpring does is the "median > shift > to percentile of 75". How can I perform this median shift to > percentile? > Maybe this is the key to find the correct values? > > Thanks in advance for any help! > > Martin > > > ----------------------------------------- > This email was sent from ATLAS Biolabs GmbH, Koeln/Cologne & Berlin. > Sitz der Gesellschaft/Registered Office: Koeln/Cologne, Germany. > Registergericht/Commercial Register Koeln/Cologne No HRB 59119, USt- > IdNr: DE251633620 > > Diese E-Mail kann Betriebs- oder Geschaeftsgeheimnisse oder sonstige > vertrauliche Informationen enthalten. Sollten Sie diese E-Mail > irrtuemlich erhalten haben, ist Ihnen eine Kenntnisnahme des > Inhalts, eine Vervielfaeltigung oder Weitergabe der E-Mail > ausdruecklich untersagt. Bitte benachrichtigen Sie uns und > vernichten Sie die empfangene E-Mail. Vielen Dank. > > This e-mail may contain trade secrets or privileged, undisclosed, or > otherwise confidential information. If you have received this e-mail > in error, you are hereby notified that any review, copying, or > distribution of it is strictly prohibited. Please inform us > immediately and destroy the original transmittal. Thank you for your > cooperation. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor