[BioC] Differential expression without replicates
whuber at embl.de
Tue Aug 28 09:34:10 CEST 2012
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?
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":
> Similarly, DESeq has a section "Working without any replicates":
> Did you try these?
> Best regards,
> 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??
>> Srinivas M. Srikanth
>> Ph.D. Student
>> Institute of Bioinformatics
>> Discoverer, 7th Floor,
>> International Technology Park,
>> Bangalore, India
>> [[alternative HTML version deleted]]
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