[BioC] wt.fun question

[Jianping Jin]

Dear BioConductor list:

I was trying to compute spot weights with a couple of small test files by 
manually data reading. The computation was done without problem. But the 
results showed zero weight for each spot, even though most of them were 
expected to get weight one . Please see the function and result below. 
Thanks a bunch for any help!

myfunRatio <- function(x, threshold=1.2) {
    okred <- abs(x[,"CH1I_MEAN"]/x[,"CH1B_MEDIAN"]) < threshold
    okgreen <- abs(x[,"CH2I_MEAN"]/x[,"CH2B_MEDIAN"]) < threshold
    as.numeric(okred & okgreen)
}

RG_ratioWeight <- 
read.maimages(file,columns=list(Rf="CH1I_MEAN",Gf="CH2I_MEAN",Rb="CH1B_MEDIAN",Gb="CH2B_MEDIAN"), 
wt.fun=myfunRatio)


> RG_ratioWeight
An object of class "RGList"
$R
     testWeight testWeight1
[1,]         10          12
[2,]         11          13
[3,]         12          14
[4,]         13          15
[5,]         14          16
[6,]         15          17
[7,]         16          18
[8,]         17          19

$G
     testWeight testWeight1
[1,]        5.0         7.0
[2,]        6.0         8.0
[3,]        7.0         9.0
[4,]        8.0        10.0
[5,]        4.3         6.3
[6,]        2.0         4.0
[7,]        3.0         5.0
[8,]        4.0         6.0

$Rb
     testWeight testWeight1
[1,]        1.0         3.0
[2,]       10.0        12.0
[3,]        3.0         5.0
[4,]        2.0         4.0
[5,]        3.0         5.0
[6,]        2.5         4.5
[7,]        5.0         7.0
[8,]        2.0         4.0

$Gb
     testWeight testWeight1
[1,]        0.5         2.5
[2,]        1.5         3.5
[3,]        2.5         4.5
[4,]        3.5         5.5
[5,]        4.5         6.5
[6,]        1.0         3.0
[7,]        2.0         4.0
[8,]        5.0         7.0

$weights
     testWeight testWeight1
[1,]          0           0
[2,]          0           0
[3,]          0           0
[4,]          0           0
[5,]          0           0
[6,]          0           0
[7,]          0           0
[8,]          0           0

$targets
                   FileName
testWeight   testWeight.txt
testWeight1 testWeight1.txt

Also I wanted to filter out some "bad" spot before I apply statistic tools, 
for example, paired t-test. Any suggestions about filtering?

JP-

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x Jianping Jin Ph.D.            x
x Bioinformatics scientist      x
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