[BioC] [Bioc] RNAseq less sensitive than microarrays? Is it a statistical issue?

[Robert Castelo]

Hi Lucia, just one comment to one of your questions.

On 5/22/13 9:57 PM, Lucia Peixoto wrote:
> In any case, I have not been able to find a study in which microarrays and
> RNAseq are compared head to head in multiple biological replicates of the
> same samples. I am not that familiar with the RNASeq literature but,
> can it be possible that when dealing with biological (not technical ) noise
> at the gene level it is still better to use microarrays?
you can find matching RNA-seq and microarray biological replicates in the
following Bioconductor experiment data package:

library(tweeDEseqCountData)
data(commonPickrell1Huang)

in the help page of those data, i.e., do help(commonPickrell1Huang), you 
will
find all details about them. i believe they could help you to explore 
this question
by applying the same pipeline you use on your own data.

cheers,
robert.

> Lucia
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> On Tue, May 21, 2013 at 6:49 PM, Wolfgang Huber <whuber at embl.de> wrote:
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>> Dear Lucia
>>
>> I just googled one of the words I had used and realised it has a much more
>> sinister meaning than I ever intended. My apologies for that very
>> unfortunate choice. A spectacularly incompetent attempt at using
>> informal/slang language in a place where it does not belong.
>>
>> You reported a large difference between the results of the 'locfdr' and
>> 'BH' methods for multiple testing correction on the microarray data. This
>> could happen (among a few other reasons) if there are problems with data
>> quality, such as batch effects, that affect the distribution of the test
>> statistic for non differentially expressed genes. How does the histogram of
>> unadjusted p-values look like? For the BH-method, it should look like a
>> mixture of a uniform between 0 and 1 (for the true nulls) and a peak at the
>> left. See also, e.g., Fig 3c in
>> http://openi.nlm.nih.gov/detailedresult.php?img=2865860_btq118f3&req=4
>>
>> The bias towards up-regulation in the RNA-Seq data is curious. It does not
>> seem to be caused by unequal library sizes. One way to get to the bottom of
>> this could be the MA-plots - how do they look like?
>>
>> Best wishes
>>          Wolfgang
>>
>> On 21 May 2013, at 23:19, Lucia Peixoto <luciap at iscb.org> wrote:
>>
>>> Dear Simon,
>>>
>>> My apologies for not being concise in explaining the problem. I am pretty
>>> new to the list and I can see that it can be frustrating to try to help
>>> someone that is not giving all the details you need to do so. I
>> appreciate
>>> your apology, since some of the initial responses to my question had a
>> very
>>> unfortunate choice of words. Going through the suggestions of the thread
>>> has been very helpful. So here is a more thorough description of what I
>>> did, as well as some observations made after taking into account
>>> suggestions:
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