[BioC] AgiMicroRna -1 filtered values

[Steve Lianoglou]

Hi,

Caveat here is that I have never processed data from these arrays
before, and I am also no Agilent software expert (ie. I have no idea
of the internal workings of their Feature Extraction Software (FES)
that you're talking about).

Comments in line:

On Wed, Feb 12, 2014 at 12:51 AM, Coonen Maarten (TGX)
<m.coonen at maastrichtuniversity.nl> wrote:
[snip]
> On the other hand, I am in doubt if I might be misinterpreting the FES-output. Which of the options below is true? I couldn't find any of this in the FES manual.
> a) FES performs QC on the probe replicates and summarizes all good probes into 1 TotalGeneSignal. Since a miRNA is represented by 30 probes, FES will always succeed in summarizing the good probes and will always generate a reliable TotalGeneSignal.
> b) FES performs QC on the probe replicates. If all probes fail to pass QC, it is unable to generate a reliable TotalGeneSignal and puts a flag in the IsGeneDetected column.

Don't know, perhaps someone else her can answer this question.

>> Also, have you checked to see if this scenario you are imagining is actually happening?
> In the sample data set it occurs multiple times, of which hsa-miR-339-5p is the first example.
> In my own data, I have seen these -1 values occurring multiple times, which made me curious to what was causing this.

Perhaps you can bring your own domain knowledge into this analysis and
you can do some data-detective work that will allow you to sidestep
knowing how precisely FES works.

There are surely miRNAs that you expect to be expressed in your
control data, and others which you know should not be. Look at where
these -1s are popping up in your control data, does this match up with
your expectations?

-steve

-- 
Steve Lianoglou
Computational Biologist
Genentech