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

Zhijin Wu zwu at jhsph.edu
Wed Sep 15 16:08:16 CEST 2004


> 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)
 
  It is surpring to me that GCRMA would give such high log2 transformed
expression for this gene. What does the distribution of expression values
look like?


> 
> 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
> 
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