[BioC] multtest error - class label problem
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?
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Wolfgang
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
the error message says it all, you specify
which corresponds to one group of size three, while mt.maxT expects two
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):
see also http://www.bepress.com/bioconductor/paper7
yuhong ning wrote:
> 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)
>> 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.
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> Search the archives:
Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber
Bioconductor mailing list
Bioconductor at stat.math.ethz.ch
Search the archives:
THIS ELECTRONIC MAIL MESSAGE AND ANY ATTACHMENT IS
CONFIDENTIAL AND MAY CONTAIN LEGALLY PRIVILEGED
INFORMATION INTENDED ONLY FOR THE USE OF THE INDIVIDUAL
OR INDIVIDUALS NAMED ABOVE.
If the reader is not the intended recipient, or the
employee or agent responsible to deliver it to the
intended recipient, you are hereby notified that any
dissemination, distribution or copying of this
communication is strictly prohibited. If you have
received this communication in error, please reply to the
sender to notify us of the error and delete the original
message. Thank You.
More information about the Bioconductor