Firstly, thanks you a lot for reply me. The strange thing is that, after doing eBayes(), in my significant probes appears some RANDOM probes. 2013/1/10 Todd Richmond <richmond.todd@gmail.com> > Hi Maria, > > The RANDOM probes on the NimbleGen arrays are randomly generated probes > with the same length and GC content characteristics as the experimental > probes on the array. They are meant to give researchers an estimate of the > signal from non-specific binding on the array. There should be no harm in > carrying them through the analysis, and the final expression value > generated for those probes can be a useful threshold for estimating which > transcripts are expressed above the background level. > > Todd > > > On Thu, Jan 10, 2013 at 6:24 AM, María José Rivas <marivas@uvigo.es>wrote: > >> Hi all, >> >> I have an experiment with 72 cDNA Nimblegen arrays. I notice that the >> arrays have some probes type RANDOM (I guess that there are control >> probes). I have performed the normalization doing: >> >> 1. Background correction >> >> RG50_bg <- backgroundCorrect (RGback, method="normexp", offset=50) >> >> RGback$printer <- list(ngrid.r=1, ngrid.c=1, nspot.r=nrow(RGback), >> nspot.c=ncol(RGback)) >> >> >> 2. Between-array normalization >> >> MA.q_50_bg <- normalizeBetweenArrays(RG50_bg, method="quantile") >> >> In the object MA.q_50_bg there are still random probes. Should the >> normalization removes them??? Or is normal doing the analysis with random >> probes??? >> >> Thanks in advance, >> >> >> -- >> >> María José Rivas Quelle (PhD. Student) >> Área de Genética (Grupo Xb2) >> Dpto. Bioquímica, Genética e Inmunología >> Facultad de Biología 36310 >> Universidad de Vigo (SPAIN) >> >> [[alternative HTML version deleted]] >> >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > > > -- > Dr Todd Richmond, PhD > richmond.todd@gmail.com > -- María José Rivas Quelle (PhD. Student) Área de Genética (Grupo Xb2) Dpto. Bioquímica, Genética e Inmunología Facultad de Biología 36310 Universidad de Vigo (SPAIN) [[alternative HTML version deleted]]