[BioC] Differential expression without replicates

[Wolfgang Huber]

Sriniva

you said "I have tried ... but not getting even a single value to be 
significant." Significance relates to the rejection of a (null) 
hypothesis in a test. What null hypothesis did you test?

- was it appropriate for the biological question you are after?
- if so, may be there is just not enough signal?

	Best wishes
	Wolfgang


Aug/28/12 9:07 AM, Mark Robinson scripsit::
> Hi Srikanth,
>
> No replicates is not an ideal situation.
>
> In the user manual, edgeR has a section "What to do if you have no replicates":
> http://www.bioconductor.org/packages/release/bioc/vignettes/edgeR/inst/doc/edgeRUsersGuide.pdf
>
> Similarly, DESeq has a section "Working without any replicates":
> http://www.bioconductor.org/packages/release/bioc/vignettes/DESeq/inst/doc/DESeq.pdf
>
> Did you try these?
>
> Best regards,
> Mark	
>
>
> On 28.08.2012, at 08:51, Srinivas M. Srikanth wrote:
>
>> HI all,
>>
>> I have paired-end RNAdata from five different tissues of the same organism,
>> I calculated the read counts using HTSeq tools and now I want to see which
>> are the transcripts which are differentially expressed (if any) among the
>> five tissues (I do not have any replicates). I have tried using edgeR and
>> DESeq packages but not getting even a single value to be significant. Can
>> anyone suggest the possibilities??
>>
>>
>> Regards,
>> Srikanth
>>
>> --
>> Srinivas M. Srikanth
>> Ph.D. Student
>> Institute of Bioinformatics
>> Discoverer, 7th Floor,
>> International Technology Park,
>> Bangalore, India
>> Mob:+919019114878
>>
>> 	[[alternative HTML version deleted]]
>>
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-- 
Best wishes
	Wolfgang

Wolfgang Huber
EMBL
http://www.embl.de/research/units/genome_biology/huber