[BioC] decideTests

[Jason Skelton]

Hi Gordon

Jason Skelton wrote:

> but the same objects either EB$t or FIT(MAarryLM) don't appear to work
> at all
>
> DT <- decideTests(EB$t, p.value=0.2, method="separate", 
> adjust.method="fdr")

Gordon Smyth wrote:

You need

DT <- decideTests(EB, p.value=0.2, method="separate", adjust.method="fdr")
-------------------------------------------------------------------------------------------------------------
sorry forgot to mention in my original email that I tried that as well

 > DT <- decideTests(EB, p.value=0.2, method="separate", 
adjust.method="fdr")
Error in decideTests(EB, p.value = 0.2, method = "separate",  :
        Need MArrayLM object


 > class(EB)
[1] "list"
 > names(EB)
[1] "df.prior"  "s2.prior"  "s2.post"   "t"         "p.value"   "var.prior"
[7] "lods"
 > summary(EB)
          Length Class  Mode
df.prior      1  -none- numeric
s2.prior      1  -none- numeric
s2.post   10080  -none- numeric
t         30240  -none- numeric
p.value   30240  -none- numeric
var.prior     3  -none- numeric
lods      30240  -none- numeric

thanks for your help

Jason



-- 
--------------------------------
Jason Skelton
Pathogen Microarrays
Wellcome Trust Sanger Institute
Hinxton
Cambridge
CB10 1SA

Tel +44(0)1223 834244 Ext 7123
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