Dear Sir / madam, I wish to have an understanding of what is One class data with cl<- c(1,1,1,1,1) in SAM and Rankproduct. I have 5 Biological replicates for a sample and I wish to apply a test to find out the significant genes. As said here no control group but only 5 biological replicates. Average intensity of each gene could be calculated then what can I do........ Kindly help me out with an answer, I am just a beginner and if there is no sense in my question kindly point out that also. With Kind regards, antony

What do you mean by "significant"? --Naomi At 10:18 AM 1/20/2009, John Antonydas Gaspar wrote: >Dear Sir / madam, > >I wish to have an understanding of what is One class data with cl<- >c(1,1,1,1,1) >in SAM and Rankproduct. > >I have 5 Biological replicates for a sample and I wish to apply a test to find >out the significant genes. As said here no control group but only 5 biological >replicates. > >Average intensity of each gene could be calculated then what can I do........ > >Kindly help me out with an answer, I am just a beginner and if there >is no sense >in my question kindly point out that also. > >With Kind regards, > >antony > >_______________________________________________ >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 Naomi S. Altman 814-865-3791 (voice) Associate Professor Dept. of Statistics 814-863-7114 (fax) Penn State University 814-865-1348 (Statistics) University Park, PA 16802-2111

On Tue, Jan 20, 2009 at 10:18 AM, John Antonydas Gaspar < gasparj@uni-koeln.de> wrote: > Dear Sir / madam, > > I wish to have an understanding of what is One class data with cl<- > c(1,1,1,1,1) > in SAM and Rankproduct. > > I have 5 Biological replicates for a sample and I wish to apply a test to > find > out the significant genes. As said here no control group but only 5 > biological > replicates. > > Average intensity of each gene could be calculated then what can I > do........ > > Kindly help me out with an answer, I am just a beginner and if there is no > sense > in my question kindly point out that also. > Unfortunately, I think your experimental design leaves a bit to be desired. Microarrays do not measure absolute expression and are only useful for measuring relative expression, in general. So, you need a comparison group in order for your data to have any real meaning. Sean [[alternative HTML version deleted]]

Dear Antony, Up and down regulation are comparative - you need some type of reference sample to determine this. With only replicates of one condition, all you can determine is the relative strength of hybridization on the microarray. As suggested by Sean, this is not even good for sorting the genes into expression levels, because the measurements on the array depend not only on transcript abundance, but also hybridization rate, cross-hybridization, labeling intensity and numerous other factors. --Naomi At 11:57 AM 1/20/2009, Antony wrote: >Naomi Altman wrote: >>What do you mean by "significant"? >> >>--Naomi >> >>At 10:18 AM 1/20/2009, John Antonydas Gaspar wrote: >>>Dear Sir / madam, >>> >>>I wish to have an understanding of what is One class data with >>>cl<- c(1,1,1,1,1) >>>in SAM and Rankproduct. >>> >>>I have 5 Biological replicates for a sample and I wish to apply a >>>test to find >>>out the significant genes. As said here no control group but only >>>5 biological >>>replicates. >>> >>>Average intensity of each gene could be calculated then what can I >>>do........ >>> >>>Kindly help me out with an answer, I am just a beginner and if >>>there is no sense >>>in my question kindly point out that also. >>> >>>With Kind regards, >>> >>>antony >>> >>>_______________________________________________ >>>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 >> >>Naomi S. Altman 814-865-3791 (voice) >>Associate Professor >>Dept. of Statistics 814-863-7114 (fax) >>Penn State University 814-865-1348 (Statistics) >>University Park, PA 16802-2111 >Dear Dr. Naomi, > >Both up regulated and down regulated genes. >With kind regards, >antony Naomi S. Altman 814-865-3791 (voice) Associate Professor Dept. of Statistics 814-863-7114 (fax) Penn State University 814-865-1348 (Statistics) University Park, PA 16802-2111