Hi,
How could I make  "read.maimages" to read the "Signal Median" from the
Imagene files  (separate R and G) files rather than the "Signal Mean" which
it does by defualt?

If you are still with me, here is some more information:
I use:
> targets <- readTargets()
> files <- targets[,c("FileNameCy3","FileNameCy5")]
> RG <- read.maimages(files, source="imagene")

to read the imagene files, Here is in an example line from the "imagene
file", the columns in bold are of interest.
-----
        Field   Meta Row        Meta Column     Row     Column  Gene ID
Annotation 1    Flag    Signal Mean     Background Mean Signal Median
Backgr
ound Median     Signal Mode     Background Mode Signal Area     Background
Area Signal Total    Background Total        Signal Stdev    Background Std
ev      Shape Regularity        Ignored Area    Spot Area       Ignored
Median  Area To Perimeter       Open Perimeter  XCoord  YCoord
Diameter
        CM-X    CM-Y    Min Diam        Max Diam        Control Failed
Control  Background contamination present        Signal contamination
present
        Ignored % failed        Open perimeter failed   Shape regularity
failed Perim-to-area failed    Offset failed   Empty spot      Negative spot

        Selected spot   Saturated spot
        A       1       1       1       1       Dye Marker      Dye
Marker      0       9.5208  0.0     0.0     0.0     0.317   0.0     48.0
69.0
        457.0   0.0     26.3636 0.0     0.6153  103.0   151.0   0.0
0.4654  0.0     236.7497        59.996  9.0     236.7081        59.496
8.5737
        8.97            0       0       0       0       0       0
0       0       0       0       0       0
---

By default it reads the "Signal Mean" files, how do I change it to read the
" Signal Median"?

The problem is that Imagene has separate files for R and G channel and so I
cannot use the stadarad format for reading, i.e, I cannot directly follow
the command from limma userguide!
> RG <- read.maimages(files,
+ columns=list(R="F635 Mean",G="F532 Mean",Rb="B635 Median",Gb="B532
Median"),
+ annotation=c("Block","Row","Column","ID","Name"))

without combining and reformatting my imagene files.

-Thanks any help.
-Lakshmanan Iyer
Res. Asst Professor of Nueroscience
Tufts University School of Medicine
Boston
MA 02111

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