[BioC] multtest error - class label problem

Yuhong Ning YNing at celgene.com
Thu Jun 22 21:47:44 CEST 2006


 

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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