[BioC] read.maimages: median intesities instead of mean

[Gordon Smyth]

Dear Lakshmanan,

To specify median foreground and background estimates, use

   RG <- read.maimages(files, source="imagene", 
columns=list(f="Signal Median",b="Background Median"))

See ?read.maimages and look at the description for the 'columns' argument.

Best wishes
Gordon

>[BioC] read.maimages: median intesities instead of mean
>Lakshmanan Iyer laxvid at gmail.com
>Tue Dec 5 22:56:26 CET 2006
>
>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