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 Background Median Signal Mode Background Mode Signal Area Background Area Signal Total Background Total Signal Stdev Background Stdev 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
