[BioC] Agilent G4112A Arrays
naomi at stat.psu.edu
Mon Jan 25 16:38:10 CET 2010
The more data one has, the fewer assumptions one needs. In the
absence of replication, you cannot get p-values without very strong
assumptions. e.g. you could assume that the vast majority of the
genes do not differentially express, that their M-values have equal
variance and that the M-values are normally distributed. Then you
could use e.g. the IQR of the M-values to estimate the sd and use
this to pick a fold cut-off for DE. You have no reasonable way to
estimate FDR with this approach, but it might be slightly better than
using 2-fold - or then again, it might not. Without replication,
there is no way to know.
At 08:53 AM 1/25/2010, Chuming Chen wrote:
>Thank you for your suggestion. My target file is as below. Although
>I couldn't fit a linear model, I still wonder whether I can do some
>statistic on M (log ratio) values and use the p-value to get the
>differentially expressed genes.
>SlideNumber FileName Cy3 Cy5
>1 B1vsT1.txt B1 T1
>2 B2vsT2.txt B2 T2
>3 B3vsT3.txt B3 T3
>4 B4vsT4.txt B4 T4
>5 B5vsT5.txt B5 T5
>Prashantha Hebbar wrote:
>>You need not to look for any other packages. Since, you do not have
>>any replicates, do not fit linear model, instead just do
>>normalization with in arrays and look at the M (log ratio) values.
>>Prashantha Hebbar Kiradi,
>>Dept. of Biotechnology,
>>Manipal Life Sciences Center,
>>--- On *Mon, 1/25/10, Chuming Chen /<chumingchen at gmail.com>/* wrote:
>> From: Chuming Chen <chumingchen at gmail.com>
>> Subject: [BioC] Agilent G4112A Arrays
>> To: bioconductor at stat.math.ethz.ch
>> Date: Monday, January 25, 2010, 6:32 AM
>> Dear All,
>> I am trying to find out the differentially expressed genes from
>> some Agilent Human Whole Genome (G4112A) Arrays data.
>> I have tried LIMMA package, but LIMMA gave the error message "no
>> residual degrees of freedom in linear model fits" and stopped. My
>> guess is that my data has no replicates in the experiment.
>> Is there any other packages I can use to find differentially
>> expressed genes which does not require replicates in the experiment?
>> Thanks for your help.
>> Bioconductor mailing list
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Naomi S. Altman 814-865-3791 (voice)
Dept. of Statistics 814-863-7114 (fax)
Penn State University 814-865-1348 (Statistics)
University Park, PA 16802-2111
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