[BioC] problems with multtest

[James MacDonald]

I believe your problem is in the call to mt.teststat. You want to subset
your data using a colon rather than an hyphen (data[,6:12] rather than
data[,6-12]). 

Best,

Jim



James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623

>>> "michael watson (IAH-C)" <michael.watson at bbsrc.ac.uk> 02/24/04
08:32AM >>>
Hi

I am having problems with multtest and it is really annoying because I
know I am being stupid!

I read a tab-delimited text file in using read.table, into a variable
called "data".

data has 12 columns, 1-5 being annotation and 6-12 (7 columns) being
actual data.

When I try:

> t <- mt.teststat(data[,6-12], c(0,0,0,1,1,1,1), test="t")

I get errors:

Error in mt.checkX(X, classlabel, test) : the number of column of X
needs to be the same as the lengtho of classlabel
 your X= 1 
 your classlabel is 0 

I just know I am being ridiculously stupid and it's probably that I
don't remember how to use R properly, but can someone tell me how to use
mt.teststat with data read in from a text file using read.table?

Thanks
Mick

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