Hi, I have used the RMA-Express upon my .CEL files and after that the NOSE RLE T2 test to filter out bad quality arrays. Yet I have so many cel- files that I can't allocate them to their t2-value (they can't be distiguished in the picture). Instead I can print the RLE and NOSE statistics separatly with their corresponding.CEL file. Now my question is, how can the t2 statistic be calculated from the NOSE and RLE statistic? Or are there any other solutions to allocate bad arrays? thank's, Noemi

Hi Noemi, Noemi Andor wrote: > Hi, > > I have used the RMA-Express upon my .CEL files and after that the > NOSE RLE T2 test to filter out bad quality arrays. Yet I have so many > cel-files that I can't allocate them to their t2-value (they can't be > distiguished in the picture). Instead I can print the RLE and NOSE > statistics separatly with their corresponding.CEL file. Now my > question is, how can the t2 statistic be calculated from the NOSE and > RLE statistic? Or are there any other solutions to allocate bad > arrays? Please take a look at the posting guide for hints how to ask questions: http://www.bioconductor.org/docs/postingGuide.html Maybe others on this list know what a NOSE RLE T2 test is, but it would be helpful for those of us who don't if you were to state the package you are using, possibly the code (and any errors) and a sessionInfo(). Otherwise, you are expecting people to do a bunch of work to decipher your question, and very few have the time or inclination to do so. Best, Jim > > thank's, > > Noemi > > _______________________________________________ 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 -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

James W. MacDonald <jmacdon at="" ...=""> writes: > > Hi Noemi, > > Noemi Andor wrote: > > Hi, > > > > I have used the RMA-Express upon my .CEL files and after that the > > NOSE RLE T2 test to filter out bad quality arrays. Yet I have so many > > cel-files that I can't allocate them to their t2-value (they can't be > > distiguished in the picture). Instead I can print the RLE and NOSE > > statistics separatly with their corresponding.CEL file. Now my > > question is, how can the t2 statistic be calculated from the NOSE and > > RLE statistic? Or are there any other solutions to allocate bad > > arrays? > > Please take a look at the posting guide for hints how to ask questions: > > http://www.bioconductor.org/docs/postingGuide.html > > Maybe others on this list know what a NOSE RLE T2 test is, but it would > be helpful for those of us who don't if you were to state the package > you are using, possibly the code (and any errors) and a sessionInfo(). > > Otherwise, you are expecting people to do a bunch of work to decipher > your question, and very few have the time or inclination to do so. > > Best, > > Jim > > > > > thank's, > > > > Noemi > > > > _______________________________________________ Bioconductor mailing > > list Bioconductor at ... > > https://stat.ethz.ch/mailman/listinfo/bioconductor Search the > > archives: > > http://news.gmane.org/gmane.science.biology.informatics.conductor > ok, well I used the HT_HG_U133A cdf -file and had about 386 .cel-files to normalize whit RMA, for which I used RMA-express. After normalizations some statistics were available to help one decide which arrays/ cel-files had bad quality: the RLE statistic: RLE = Run Length Encoding (I think) and the NOSE statistic The T2 RLE NOSE statistic combines the two statistics into one single number, which is plottet for every cel-file. Yet there are to many cel-files to read them from the x-achsis of the plot, so I have to figure out some other way to associate each cel file with it's corresponding statistic. As there is an option to print the NUSE and RLE statistics separatly, I can use them to calculate the so called "t2 nuse RLE" statistic: So what I have is: NUSE: cel-file: 1 2.... min a1 LQ a2 mean a3 UQ a4 max a5 RLE cel-file: 1 2.... min b1 LQ b2 mean b3 UQ b4 max b5 What I want is: T2 NUSE RLE cel-file 1 2... t2 ? part of the log-file: ************* Reading in data Opening CDF and CEL files Done Reading in datafiles Choose Preprocessing Steps Carrying out Analysis Background Adjusting. Normalizing Using Quantile Normalization. Summarizing Using PLM. Done computing expression measure using PLM. Visualizing QC statistics ************* I couldn't find that information anywhere, so I thought some of you who used RME-express, have some hints. best, Noemi