Question: read.maimages: median intensities instead of mean
gravatar for Lakshmanan Iyer
10.9 years ago by
United States
Lakshmanan Iyer250 wrote:


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
MA 02111


ADD COMMENTlink modified 11 days ago by Gordon Smyth32k • written 10.9 years ago by Lakshmanan Iyer250
gravatar for Gordon Smyth
11 days ago by
Gordon Smyth32k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth32k wrote:

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

ADD COMMENTlink written 11 days ago by Gordon Smyth32k
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