[BioC] spot filtering

Gordon K Smyth smyth at wehi.EDU.AU
Sat Jul 23 14:29:28 CEST 2005

> 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)


> 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

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