Question: RLE question for QC
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gravatar for D.Enrique ESCOBAR ESPINOZA
13.0 years ago by
HI, In RLE boxplots we expect to see values centered on zero showing small inter-quartile range. Do anyone know what threshold is widely acceptable? (for median or IQR values) Thanks. ______________________________________________________________________ ______________ Cheap talk?
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ADD COMMENTlink modified 13.0 years ago by Alvord, Greg DMS [Contr]160 • written 13.0 years ago by D.Enrique ESCOBAR ESPINOZA360
Answer: RLE question for QC
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gravatar for Wolfgang Raffelsberger
13.0 years ago by
Wolfgang Raffelsberger160 wrote:
Hi, with good experiments I see an IQR of apr -0.2 to +0.2 . But I rather look if all the arrays of this study have homogeneous RLE IQRs and medians, since typical RLE IQR also reflect (in part) the nature of the samples tested. Basically, if your samples (and so the corresponding fluorescence signal intensities) are very much alike you tend to get smaller RLE IQRs. So there may be an explanation based on the experimental details to consider ! Keep in mind that - although the RLE is indeed very useful - it's not the sole QC criteria. Cheers, Wolfgang D.Enrique ESCOBAR ESPINOZA a ?crit : > HI, > > In RLE boxplots we expect to see values centered on zero showing > small inter-quartile range. > > Do anyone know what threshold is widely acceptable? > (for median or IQR values) > > Thanks. > > > > ____________________________________________________________________ ________________ > Cheap talk? > > _______________________________________________ > 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 > > > > > . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Wolfgang Raffelsberger, PhD Laboratoire de BioInformatique et G?nomique Int?gratives IGBMC 1 rue Laurent Fries, 67404 Illkirch Strasbourg, France Tel (+33) 388 65 3314 Fax (+33) 388 65 3276 wolfgang.raffelsberger at igbmc.u-strasbg.fr
ADD COMMENTlink written 13.0 years ago by Wolfgang Raffelsberger160
Answer: RLE question for QC
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gravatar for Alvord, Greg DMS [Contr]
13.0 years ago by
Alvord, Greg DMS [Contr]160 wrote:
Enrique - We recently performed a series of elaborate quality control assessment procedures on probe level data for the soybean genome (24 CEL files under different strains and time conditions). Our RLE plots were nicely centered around zero, and the boxes (interquartile ranges) in the box plots ranged from -0.2 to 0.2 logs. Greg W. Gregory Alvord, Ph.D. Director, Statistical Consulting Services Computer and Statistical Services National Cancer Institute at Frederick Post Office Box B Frederick, MD 21702-1201 Phone: 301.846.5101 Facsimile: 301.846.6196 E-Mail gwa at css.ncifcrf.gov -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of D.Enrique ESCOBAR ESPINOZA Sent: Tuesday, November 28, 2006 5:52 PM To: bioconductor at stat.math.ethz.ch Subject: [BioC] RLE question for QC HI, In RLE boxplots we expect to see values centered on zero showing small inter-quartile range. Do anyone know what threshold is widely acceptable? (for median or IQR values) Thanks. ______________________________________________________________________ __ ____________ Cheap talk? _______________________________________________ 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
ADD COMMENTlink written 13.0 years ago by Alvord, Greg DMS [Contr]160
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