[BioC] Help: LIMMA-decideTests and lfc option

[James MacDonald]

I think there is a quote in the fortunes package that covers this:

library(fortunes)
fortune("yoda")

should answer the question of 'Is it possible'.

However, if what you really are asking is 'Does decideTests() do a conditional test?', then no. The tests are all on individual contrasts. If you want something different you will have to code it up yourself.

Best,

Jim



James W. MacDonald, M.S.
Biostatistician
Hildebrandt Lab
8220D MSRB III
1150 W. Medical Center Drive
Ann Arbor MI 48109-0646
734-936-8662
>>> Sherosha Raj <sherosha at gmail.com> 01/23/09 5:40 PM >>>
Hi Jim
 Thank you for the clarification. Is it possible to have a conditional
selection based on the lfc in decideTests?
Eg. if I had three contrasts and there is a probeset with lfc that satisfies
my cutoffs in just ONE contrast but not in the others, and I would still
like it to be considered?


Thank you again.
Regards,
Sherosha


2009/1/23 James MacDonald <jmacdon at med.umich.edu>

> Hi Sherosha,
>
> The lfc argument applies to all the contrasts you have made individually.
> So for instance if you have three contrasts and for one probeset they were
> (-1.5, 0.3, and 1.1) and you set lfc = 1, then the first and third would
> pass that filter and the second would not.
>
> Best,
>
> Jim
>
> James W. MacDonald, M.S.
> Biostatistician
> Hildebrandt Lab
> 8220D MSRB III
> 1150 W. Medical Center Drive
> Ann Arbor MI 48109-0646
> 734-936-8662
> >>> Sherosha Raj <sherosha at gmail.com> 01/22/09 2:28 PM >>>
> Hello everyone
>
> I am unsure how to interpret the lfc option in the multiple testing
> algorithm decideTests:
> decideTests(object,method="separate",adjust.method="BH",p.value=0.05,lfc=0)
>
> The explanation given is:
> "If lfc>0 then contrasts are judged significant only when the
> log2-fold change is at least this large in absolute value. For
> example, one might choose lfc=log2(1.5) to restrict to 50% changes or
> lfc=1 for 2-fold changes. In this case, contrasts must satisfy both
> the p-value and the fold-change cutoff to be judged significant."
>
> What is meant exactly? Is it within a particular contrast that the
> log2FC>0 for a particular probeset? Or is it comparing across all the
> contrasts specified?
>
> If some one could offer a clarification  I would be most grateful.
> Thank you.
>
> --
> Regards,
> Sherosha
>
> --
> Regards,
> Sherosha
>
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