[BioC] LimmaGUI Spot Quality

[Elizabeth Brooke-Powell]

Sorry James,

Here are the columns titles:

ROW
COL
SUBGRIDROW
SUBGRIDCOL
SPOTNUM
BLOCK
NAME
ID
CONFIDENCE
FLAG
MAN EXCL
AMPCH1
AMPCH2
RATIO CH1/CH2
LOG2RATIO CH1/CH2
LOG10RATIO CH1/CH2
RATIO CH2/CH1
LOG2RATIO CH2/CH1
LOG10RATIO CH2/CH1
SUM
PELROW
PELCOL

I have previously used the other function in LimmaGUI and used AMPCH1 and
AMPCH2 as the signal channels, there is no background data as the background
is taken account of in the model. The column labelled CONFIDENCE is
obviously the one in question. 

Thanks for your help,

Liz

-----Original Message-----
From: James Wettenhall [mailto:wettenhall at wehi.edu.au] 
Sent: 02 July 2004 16:42
To: Elizabeth Brooke-Powell
Cc: bioconductor at stat.math.ethz.ch
Subject: RE: [BioC] LimmaGUI Spot Quality

Liz,

On Fri, 2 Jul 2004, Elizabeth Brooke-Powell wrote:
> adjust the model appropriately. I am not sure in this case that pretending
> to have GenePix will work as the numbers are not a simple 0 or 1 (good or

No, sorry I didn't mean to imply that you would be able to just 
use the GenePix option in limmaGUI as is.  I just thought it 
might by helpful for you to learn how weights can be defined 
(for _GenePix_ data), based on GenePix spot flags.  Notice that 
the weights we define for the GenePix flags are between 0 and 
1, just as your "quality weights" already are.  But after we 
process GenePix data, the number of _different_ values in the 
weights column would be small, e.g. in this weights vector: 
(1,1,1,1,0.1,1,1,1,1,1,1,0,1,1,1,1,1,0.1,0.1,1,1,1,1,1), 
there are only three _different_ weight values (0, 0.1 and 1),
whereas for your data, the column of weights (between 0 and 1) 
could contain lots of different weight values between 0 and 1 
for the different genes.

I don't think you have told us the column name of this 
quality weight yet.  

Maybe you should ask the statistician who designed this 
quality weighting how he/she intended that it be used in  
normalization.  But it can probably be used directly in 
limma's normalization, and all you would have to do is tell us 
the appropriate column names which limma would need to read in 
for your data (Rf, Rb, Gf, Gb and Spot-Quality-Weighting) and 
then we can add an option to limma/limmaGUI to allow it to read 
in the appropriate columns for BlueFuse including the quality 
weights.

There are no plans at the moment to add a custom-dialog to 
limmaGUI for reading in an arbitrary column of weights from your 
raw image-analysis files.  But if you want to start combining 
the command-line interface with the GUI interface, you could 
read the weights into RG$weights in limmaGUIenvironment.  Then 
they would be automatically used for normalization.

(1) From the R console :
RG <- get("RG",envir=limmaGUIenvironment)
names(RG)
RG$weights <- ...
names(RG)
assign("RG",RG,limmaGUIenvironment)

OR 
(2) From the "Evaluate R Code menu:
RG$weights <- ...

(In case (2), when using the "Evaluate R Code" menu, your R 
commands are automatically evaluated in limmaGUIenvironment 
which contains all of your microarray data objects used by 
limmaGUI.)

Regards,
James