Laurent Gautier <laurent@cbs.dtu.dk> wrote: > One should keep in mind the assumption behind many of the normalization > techniques: "most of the genes are not differentially expressed across > the > experiments". Filtering before normalization/scaling should be done with > that in mind. Hi all. I'm a novice,... may be this is he reason why I'm loosing myself.. What is a "low espressed spot"? It seems a problem of logic. It seems to me that on one side we say that it not an expressed gene (= we can not consider as an expressed gene), it's more likely dued to noise (background,...). On the other side we say that, however, it's actually an expression and good for normalizing. Of course a non expressed gene is also not differentially expressed... Are good enougth for normalization and not enougth for other analysis? Is it another cut-off problem?? Absent - So and so (for normalizing yes, other analysis no) - Present - AleA ----------------------------------------------------- Salve, il messaggio che hai ricevuto ? stato inviato per mezzo del sistema di web mail interfree. Se anche tu vuoi una casella di posta free visita il sito http://club.interfree.it Ti aspettiamo!

On Mon, 2 Jun 2003 alea@interfree.it wrote: > > Laurent Gautier <laurent@cbs.dtu.dk> wrote: > > > One should keep in mind the assumption behind many of the normalization > > techniques: "most of the genes are not differentially expressed across > > the > > experiments". Filtering before normalization/scaling should be done with > > that in mind. > > Hi all. > I'm a novice,... may be this is he reason why I'm loosing myself.. > What is a "low espressed spot"? > It seems a problem of logic. a better way to say it is "low intensity spot". low intesities are usually due to low expression of the gene or probe represented by the spot. > > It seems to me that on one side we say that it not an expressed gene (= we can not consider as an expressed gene), it's more likely dued to noise (background,...). > but where (and how) do you draw the line? > On the other side we say that, however, it's actually an expression and good for normalizing. > Of course a non expressed gene is also not differentially expressed... what if its non-expressed on one array and expressed on another? i would call this differentially expressed. > > Are good enougth for normalization and not enougth for other analysis? > Is it another cut-off problem?? > > Absent - > So and so (for normalizing yes, other analysis no) - > Present - > normalization techiniques that use all genes or probes appear to work succesfully in practice. papers by dudoit, bolstad, aastrad, li and wong, huber, and various others demonstrate this. > AleA > > > > ----------------------------------------------------- > > Salve, il messaggio che hai ricevuto > č stato inviato per mezzo del sistema > di web mail interfree. Se anche tu vuoi > una casella di posta free visita il > sito http://club.interfree.it > Ti aspettiamo! > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >

Hi all! I have some problems in importing data in bioconductor from a matrix in eisen format. Can anyone help me? Thank you

Dear all: Excuse me. After installing bioconductor, I found a command, widget.marrayInput, which is a GUI for marrayInput on webpage of bioconductor. The command is shown on the slide of the short course "Analyzing DNA Microarray Data Using Bioconductor". However, I could't find its documentation in the package list. Could you tell me where I can get it? Besides, I wonder that if there are such commands as "widget.marrayInput" for marrayNorm or other pre-proccesing packages. Hopefully, I could hear from you soon :). Thanks for your help a lot! best beckon ------------------------------------------------- This mail sent through NCTU WebMail System: https://webmail.nctu.edu.tw