Dear Dr. Huber,

I want to see that if there is any difference in the expression levels of
isoforms in different tissues (five in this case). So, the null here is
there is no significant difference in the expression levels across tissues.
I am trying to get the top differentials and than try to correlate the data
with proteogenomics.

Regards,
Srikanth

On Tue, Aug 28, 2012 at 1:04 PM, Wolfgang Huber <whuber@embl.de> wrote:

> 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<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<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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>>>
>>
>> ----------
>> Prof. Dr. Mark Robinson
>> Bioinformatics
>> Institute of Molecular Life Sciences
>> University of Zurich
>> Winterthurerstrasse 190
>> 8057 Zurich
>> Switzerland
>>
>> v: +41 44 635 4848
>> f: +41 44 635 6898
>> e: mark.robinson@imls.uzh.ch
>> o: Y11-J-16
>> w: http://tiny.cc/mrobin
>>
>>
>
> --
> Best wishes
>         Wolfgang
>
> Wolfgang Huber
> EMBL
> http://www.embl.de/research/**units/genome_biology/huber<http://www.embl.de/research/units/genome_biology/huber>
>
>
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> science.biology.informatics.**conductor<http://news.gmane.org/gmane.science.biology.informatics.conductor>
>



-- 
Srinivas M. Srikanth
Ph.D. Student
Institute of Bioinformatics
Discoverer, 7th Floor,
International Technology Park,
Bangalore, India
Mob:+919019114878

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