[BioC] LIMMA decideTests result zero from contrast matrix

Ekta Jain Ekta_Jain at jubilantbiosys.com
Tue May 8 06:42:32 CEST 2012

Hi Steve,
I have been using the lists for a long time now and was never told off before for emailing to both R (r-help at r-project.org) and Bioconductor(bioconductor at r-project.org) at the same time. I think, it saves time and is the quickest way to get your query across people since not everyone can be on both the lists.

I can most certainly try and post to the relevant list but 95% of the time I am then told to post to the other list since the topic is not relevant here. I am afraid this process at times takes up an extra day before some good soul out there reads my post and offers help. I am sorry but I did not mean to stress anyone.

I could have googled 'cross-posting' but I meant to ask in this context and not as a general rule. Ideally, I wouldn't rely on Wikipedia for all information :-).

I've tried changing things and no results. I reckon, it's probably down to the data I have. It works fine on another dataset with decent p-values. I am clueless why it wouldn't work.

You asked me for adjusted p-values, why? 

Thanks a lot !


-----Original Message-----
From: Steve Lianoglou [mailto:mailinglist.honeypot at gmail.com] 
Sent: 07 May 2012 19:00
To: Ekta Jain
Cc: bioconductor at r-project.org
Subject: Re: [BioC] LIMMA decideTests result zero from contrast matrix

Hi Ekta,

On Sun, May 6, 2012 at 11:38 PM, Ekta Jain <Ekta_Jain at jubilantbiosys.com> wrote:
> Hi Steve,
> What do you mean by "cross-post between mailing list" ? I usually mail to both Bioconductor and R to avoid the suggestion to email the 'correct' place. More so since i was not sure who would be better able to answer my question.

I mean putting multiple mailing lists in the to and cc fields of the
same email -- it's frowned upon. A quick googling of "cross posting
mailing lists" will get you more info. Heck, there's even a wikipedia
page :-)


So -- what you "usually" do: bad :-)

If your question has to do w/ some bioinformatics topic (like this
question), then post here. If it has nothing to do w/ bioinformatics,
but more about some base R thing, eg: "how come I can't read this
table" or whatever, then go to R-help.

> Adjusted p-values are pretty bad - 0.999540865122392

As Jim also pointed out, I reckon this is why nothing's popping up in
your venn diagram.


Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact
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