[BioC] decideTests

[Gordon K Smyth]

On Thu, November 4, 2004 8:16 pm, Jason Skelton said:
> 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

Well, the error message is pretty self-explanatory!  You need to give it an object of class
"MArrayLM", i.e., you need to give it output from lmFit() and eBayes(), as in all the examples in
the User's Guide.

You didn't say how you created FIT and EB.  I am guessing now that you used lm.series() or
gls.series().  I am been phasing these functions out of the user-interface for a long time -- they
are lower-level functions that produce unclassed list objects.  There is no need for you to use
them.  So far I have been writing functions that are tolerant of whether the input arguments are
formally classed or not, but in future I may not do that.

So, please, use lmFit(), not lm.series().

Gordon

>  > 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
> Fax +44(0)1223 494919
> --------------------------------