[BioC] Calculate BCV in edgeR - sample without replicates

[Atul]

Hi Ryan,

Thanks for the explanation. Best.

Atul


On 12/19/2013 02:01 PM, Ryan wrote:
> Hi Atul,
>
> This has been asked before in a slightly different context, but in 
> general it is acceptable to further subdivide your groups after 
> estimating dispersions. At worst, you will end up with an overly 
> conservative test because your dispersion estimation will overestimate 
> the dispersion for your final set of groups. In your case, you are 
> estimating dispersions with one group and then splitting that group 
> into two.
>
> -Ryan
>
> On 12/19/13, 10:03 AM, Atul Kakrana wrote:
>> 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
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>      [[alternative HTML version deleted]]
>>>>
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>
>
>