[BioC] multtest error - class label problem

[Katherine Pollard]

Yuhong,

You can use multtest for 1 group data, with the boostrap null distribution 
(MTP function), but not wiht the permutation nulldistribution. If your 
sample size is small, however, the bootstrap null distribution will not 
work. With n=3, it really does not make sense to do resampling based 
multiple testing. That said, you might try MTP with

test="t.onesamp"
standarize=FALSE
robust=TRUE

This will do a 1 sample wilcoxon signed rank test more or less. You might 
just use wilcox.test also, and forget the resampling.

Best,
Katie

On Thu, 22 Jun 2006, Yuhong Ning wrote:

>
>
> Thank you, Wolfgang.
>
> I did use limma to analyze the same data set days ago, and hoped to use
> "multtest" for a validation of my limma result. So I can't use
> "multtest" for one group data?
>
> Yuhong
>
>
>
>
>
>
> -----Original Message-----
> From: bioconductor-bounces at stat.math.ethz.ch
> [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Wolfgang
> Huber
> Sent: Thursday, June 22, 2006 10:47 AM
> To: yuhong ning
> Cc: Katherine S. Pollard; bioconductor at stat.math.ethz.ch
> Subject: Re: [BioC] multtest error - class label problem
>
> Dear Yuhong,
>
> the error message says it all, you specify
> 	clabel<-c(0,0,0)
> which corresponds to one group of size three, while mt.maxT expects two
> groups.
>
> Katie - There seems to be a buglet in the code that produces the error
> message, making it a bit hard to read, could you check this?
>
> If you only have three replicates, I would recommend to a moderated
> t-statistics such as available with the limma package (eBayes function):
>
>  library(limma)
>  ? eBayes
>  example(eBayes)
>
> see also http://www.bepress.com/bioconductor/paper7
>
>
> Best wishes
>  Wolfgang
>
>
>
> yuhong ning wrote:
>> Hi,
>>
>> I am using "multtest" to analyze proteomics data. The experiment is to
>
>> compare protein differential expression between Wild Type and mutant
>> cell types. MS software generates a ratio of intensity of
>> heavy-isotope/light-isotope which correspondent to wild type vs.
>> mutant. It is a triplicate experiment, but for some proteins, ratio
>> data are missing. My R script is very simple:
>>
>>> dd<-read.delim("log2_data.txt", header=TRUE)
>>> clabel<-c(0,0,0)
>>> res<-mt.maxT(dd, clabel, B=20)
>> Error in mt.checkclasslabel(classlabel, test) :
>>         in t test, every number in class label needs to be 0 or 1 and
>> neither of the 0 set or 1 set can be empty set  The folllowing is your
>
>> setting of classlabel 0 in t test, every number in class label needs
>> to be 0 or 1 and neither of the 0 set or 1 set can be empty set  The
>> folllowing is your setting of classlabel 0 in t test, every number in
>> class label needs to be 0 or 1 and neither of the 0 set or 1 set can
>> be empty set  The folllowing is your setting of classlabel 0
>>
>>
>> Could any one help?
>>
>> Thanks a lot.
>>
>> yuhong
>>
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>
>
> --
> ------------------------------------------------------------------
> Wolfgang Huber  EBI/EMBL  Cambridge UK  http://www.ebi.ac.uk/huber
>
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