> Date: Fri, 22 Jul 2005 11:41:50 -0500 > From: etbp2 at borcim.wustl.edu (Brooke-Powell, Elizabeth) > Subject: [BioC] spot filtering > To: <bioconductor at="" stat.math.ethz.ch=""> > > Michael, > > I was interested in how you flag your data, when you load your files do you > read in your flag column as part of a standard GenePix type output file, so > limma uses it when the linear model is fit? I use BlueFuse and its flag > column is quite different from GenePix and the like and at present not able > to be used in limma. I think I'd use the 'CONFIDENCE' column. In limma 2.0.4, I'd use f <- function(x) x$CONFIDENCE RG <- read.maimages(files, source="bluefuse", wt.fun=f) Gordon > I am wondering how to mark (flag) the bad data and > either leave it in or what to put in the data file to get the data ignored > i.e. can you put NA in place of the data point and have it ignored? Is it as > simple as creating a new flag column converting the BlueFuse flags into > GenePix like flags? If I load the data file using the other file type option > in LimmaGUI it doesn't allow me to tell it where there is a flag column. Is > this something that could be fixed assuming the flag column conforms to the > GenePix style of 0, +1 and -1 calls? > > Thanks for the help and insight, > > Liz