[BioC] Calculate BCV in edgeR - sample without replicates

[Atul Kakrana]

Hi Ryan,

Many thanks for your reply. Do you think it's theoretically correct to
change the grouping before exact test for norm.tags2? I have no idea
about how estimateDisp() works due to my non-statistics background and
just want to make sure that I am not making any mistake.

Best

Atul


On 12/18/2013 05:55 PM, Ryan wrote:
> Hi Atul,
>
> I believe that all you need to do is to restore the correct grouping
> before calling exactTest, i.e. something like:
>
> norm.tags2$samples$groups = c(1,2)
>
>
> -Ryan
> On Wed Dec 18 13:08:12 2013, Atul Kakrana wrote:
>> Hi All,
>>
>> I am working on sRNA-seq data and with no replicates and using edgeR to
>> identify differentially expressed tags and using an arbitrary BCV value
>> (0.3) based on suggestion in edgeR manual:
>>
>> "Simply pick a reasonable dispersion value, based on your experience
>> with similar data, and use that for exactTest or glmFit. Typical values
>> for the common BCV (square- root-dispersion) for datasets arising from
>> well-controlled experiments are 0.4 for human data, 0.1 for data on
>> genetically identical model organisms or 0.01 for technical
>> replicates. "
>>
>> But I came across this post which mentions a conservative way to
>> calculate BCV:
>> [BioC] EdgeR: general advice on using edgeR for sRNA analysis:
>> https://stat.ethz.ch/pipermail/bioconductor/2013-August/054239.html
>>
>> I am getting an error calculating BCV using the approach discussed in
>> post. Here is my code
>>
>> norm.tags2 <- norm.tags
>> norm.tags2$samples$groups = c(1,1)
>> norm.tags2 <-
>> estimateDisp(norm.tags2,robust=TRUE,winsor.tail=c(0.05,0.2))
>> results = exactTest(norm.tags,dispersion=norm.tags2$trended.dispersion)
>>
>> Error in exactTest(norm.tags, dispersion =
>> norm.tags2$trended.dispersion) :
>>    At least one element of given pair is not a group.
>>   Groups are:
>>
>> I believe the error is because I have grouped samples as replicates for
>> calculating BCV while they are being compared against each other in
>> exactTest. Can I calculate the dispersion values from samples? rather
>> than setting arbitrarily?
>>
>> I would really appreciate any help. Awaiting reply.
>>
>> Atul
>>
>>
>>
>>
>>
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>>
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>
>