[BioC] One class data

Naomi Altman naomi at stat.psu.edu
Tue Jan 20 19:50:08 CET 2009

Dear Antony,

Up and down regulation are comparative - you need some type of 
reference sample to determine this.  With only replicates of one condition,
all you can determine is the relative strength of hybridization on 
the microarray.  As suggested by Sean, this is not even good for 
sorting the genes into
expression levels, because the measurements on the array depend not 
only on transcript abundance, but also hybridization rate, 
cross-hybridization, labeling
intensity and numerous other factors.


At 11:57 AM 1/20/2009, Antony wrote:
>Naomi Altman wrote:
>>What do you mean by "significant"?
>>At 10:18 AM 1/20/2009, John Antonydas Gaspar wrote:
>>>Dear Sir / madam,
>>>I wish to have an understanding of what is One class data with 
>>>cl<- c(1,1,1,1,1)
>>>in SAM and Rankproduct.
>>>I have 5 Biological replicates for a sample and I wish to apply a 
>>>test to find
>>>out the significant genes. As said here no control group but only 
>>>5 biological
>>>Average intensity of each gene could be calculated then what can I 
>>>Kindly help me out with an answer, I am just a beginner and if 
>>>there is no sense
>>>in my question kindly point out that also.
>>>With Kind regards,
>>>Bioconductor mailing list
>>>Bioconductor at stat.math.ethz.ch
>>>Search the archives: 
>>Naomi S. Altman                                814-865-3791 (voice)
>>Associate Professor
>>Dept. of Statistics                              814-863-7114 (fax)
>>Penn State University                         814-865-1348 (Statistics)
>>University Park, PA 16802-2111
>Dear Dr. Naomi,
>Both up regulated and down regulated genes.
>With kind regards,

Naomi S. Altman                                814-865-3791 (voice)
Associate Professor
Dept. of Statistics                              814-863-7114 (fax)
Penn State University                         814-865-1348 (Statistics)
University Park, PA 16802-2111

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