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

[Steve Lianoglou]

Hi Lucia,

On Wed, May 22, 2013 at 12:57 PM, Lucia Peixoto <luciap at iscb.org> wrote:
[snip]
> 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?

There are likely better ones, but here's the first one that fit your
criteria from a google scholar search:

Evaluating Gene Expression in C57BL/6J and DBA/2J Mouse Striatum Using
RNA-Seq and Microarrays
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0017820

The methods section for the RNA-seq data begins like so:

"""
Total RNA from 21 male mice (10 B6 and 11 D2) was provided to the
Oregon Health & Science University Massively Parallel Sequencing
Shared Resource facility [25] for transcriptome sequencing (NCBI SRA
accession number: SRA026846.1).
"""

HTH,
-steve


--
Steve Lianoglou
Computational Biologist
Department of Bioinformatics and Computational Biology
Genentech