Dear Rich, Thank you so much for your inputs. Regards, Karthik On Thu, Jun 14, 2012 at 7:24 PM, Richard Friedman < friedman@cancercenter.columbia.edu> wrote: > Dear Karthik, > > > On Jun 14, 2012, at 9:45 AM, Karthik K N wrote: > > Dear Rich, >> >> Thanks a lot for your reply. I am just worried because somewhere I >> remember reading that LIMMA can't be used without replicates ( in case of >> mRNA microarray analysis); so just wanted to check if it is the same with >> AgiMicroRna package also. >> > > I think that LIMMA can be used without replicates but it cannot give you a > p-value. I suggest > a minimum of 3 biological replicates per sample. > > > >> Also, Do you think it is a good idea to carry out GeneSpring analysis >> upon the data analyzed by biocondcutor? Will it give any statistically more >> reliable output that using either of them alone? >> > > I do not know how GeneSpring normalizes Agilent MicroRNA data but > AgiMicroRna is the best way to > normalize such data described in the open literature of which I am aware. > The statistical methods in LIMMA are more reliable than those in > GeneSpring in general. However > with only one replicate of each condition neither program can give a > p-value, only a log2FC. > You can get the same result in an excel spreadsheet, > > > > >> Also, since the data from bioconductor has already normalized, if we >> again give this as an input file for genespring and go on with analysis, >> then do we need to do normalization step again in GeneSpirng? Won't this be >> a double-normalization? >> > > I haven't used GeneSpring for a long time. I am not sure what it will do > to your data. > If you only have one replicate you might consider using AgiMicroRNA to > normalize and Excel to > compute the log2FC. > > Best wishes, > Rich > > > > > >> I am new to R/Bioconductor, so any suggestions from you will be extremely >> helpful. >> >> Thanks a lot, >> >> Karthik >> >> >> On Thu, Jun 14, 2012 at 7:08 PM, Richard Friedman <friedman@cancercenter.>> **columbia.edu <friedman@cancercenter.columbia.edu>> wrote: >> Dear Karthik, >> >> I am pretty sure that AgiMicroRna will normalize one treated and >> one control. The problem comes later in terms of the reproducibility >> of the effect, or to phrase it differently, whether the observed effect >> is a general statement about the population of treatments and controls. >> In more specific terms, the subsequent LIMMA analysis will not >> compute a p-value. >> >> With hopes that this helps, >> Rich >> ------------------------------**------------------------------ >> Richard A. Friedman, PhD >> Associate Research Scientist, >> Biomedical Informatics Shared Resource >> Herbert Irving Comprehensive Cancer Center (HICCC) >> Lecturer, >> Department of Biomedical Informatics (DBMI) >> Educational Coordinator, >> Center for Computational Biology and Bioinformatics (C2B2)/ >> National Center for Multiscale Analysis of Genomic Networks (MAGNet) >> Room 824 >> Irving Cancer Research Center >> Columbia University >> 1130 St. Nicholas Ave >> New York, NY 10032 >> (212)851-4765 (voice) >> friedman@cancercenter.**columbia.edu <friedman@cancercenter.columbia.edu> >> http://cancercenter.columbia.**edu/~friedman/<http: cancercenter.c="" olumbia.edu="" ~friedman=""/> >> >> "School is an evil plot to suppress my individuality" >> >> Rose Friedman, age15 >> >> >> >> >> >> >> >> >> >> >> >> On Jun 14, 2012, at 5:51 AM, Karthik K N wrote: >> >> Dear Members, >> >> Do we need replicates to carry out analysis with AgiMicroRna package in >> bioconductor? I have one control and one treated samples. Can I go ahead >> with AgiMicroRna with these two datasets? >> >> Thank you. >> >> -- >> Karthik K.N >> >> [[alternative HTML version deleted]] >> >> ______________________________**_________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.e="" thz.ch="" mailman="" listinfo="" bioconductor=""> >> Search the archives: http://news.gmane.org/gmane.** >> science.biology.informatics.**conductor<http: news.gmane.org="" gmane="" .science.biology.informatics.conductor=""> >> >> >> >> >> -- >> Karthik K.N >> Cancer Discovery Biology Laboratory >> Division of Molecular Medicine >> Amrita Center for Nanosciences and Molecular Medicine >> Amrita Institute of Medical Sciences >> AIMS-Ponekkara (P.O), Kochi >> Cochin, Kerala - 682 041 >> +91-484-280 1234 x 8720 >> +91-9400193907 >> >> > -- Karthik K.N Cancer Discovery Biology Laboratory Division of Molecular Medicine Amrita Center for Nanosciences and Molecular Medicine Amrita Institute of Medical Sciences AIMS-Ponekkara (P.O), Kochi Cochin, Kerala - 682 041 +91-484-280 1234 x 8720 +91-9400193907 [[alternative HTML version deleted]]