[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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