[BioC] Expression levels in GCRMA and MAS5.0 and cut-off

[Jordi Altirriba Gutiérrez]

Dear Bioconductor users,

I have 12 Affymetrix arrays with a factorial design 2 x 2.
I've been using the package Affy, GCRMA and Limma to analize my data.
Now I have a list of diferential expressed genes for each factor and I was 
wondering if some of these genes have an expression level in all the arrays 
near to the background for removing them from my final list (it's an 
"eyeballometric" method and the cut-off is arbitrary, I know).
So, I've been observing the expression levels of some genes in Affy and in 
GCRMA and I've observed some differences. I expected some differences, but 
they are bigger than I thought.

For exemple, gene 1370943_at:

Expression levels for MAS5.0 (not log2 transformed)
Array names:           DNT1.CEL   DNT2.CEL ...until 12
Expression levels:      4.2            7.3          
------------->"eyeballometrically" I had removed this gene
(there isn't any other gene in my list with lower expression levels)

Expression levels for GCRMA (log2 transformed)
Array names:           DNT1.CEL            DNT2.CEL       ....until 12
Expression levels:     20.68613483	       27.21562194 ->"eyeballometrically" 
I hadn't removed this gene (there are other genes in my list with values 
between 6 and 7)

Moreover, the expression levels of the Perfect Match and Miss Match are:

Expression levels for pm:
>pm(data,"1370943_at")
                    DNT1.CEL DNT2.CEL ......until 12
1370943_at1     503.8    434.3
1370943_at2    1084.5    857.8
1370943_at3     413.3    378.5
1370943_at4     102.8    119.5
1370943_at5     339.3    325.0
1370943_at6     380.5    327.3
1370943_at7     154.5    117.5
1370943_at8     197.5    195.0
1370943_at9      70.8     77.5
1370943_at10     55.5     62.0
1370943_at11     55.0     72.0

Expression levels for mm:
>mm(data,"1370943_at")
                     DNT1.CEL DNT2.CEL ....until 12
1370943_at1     645.5    535.3
1370943_at2    1250.5   1119.0
1370943_at3     415.0    499.5
1370943_at4     144.5    127.8
1370943_at5     281.8    291.0
1370943_at6     448.8    444.0
1370943_at7     196.3    174.3
1370943_at8     127.0    131.5
1370943_at9      71.3     75.0
1370943_at10     61.8     73.0
1370943_at11     61.3     81.3

Therefore, I suppose I should remove this gene from my list, should I? Is 
there any way to stablish a cut-off for the lower expressing genes? The 
"eyeballometric" system is too subjective.

Thank you very much for you time and help.
Yours faithfully,

Jordi Altirriba
PhD student
Hospital Clinic - Barcelona - Spain