[BioC] AgiMicroRna -1 filtered values

Steve Lianoglou lianoglou.steve at gene.com
Tue Feb 11 15:26:43 CET 2014


Hi,

On Tue, Feb 11, 2014 at 12:04 AM, Coonen Maarten (TGX)
<m.coonen at maastrichtuniversity.nl> wrote:
> Dear mailing list,
>
> I'm using the AgiMicroRna-package to analyze my Agilent microRNA arrays.
> It occurred to me that the ProcessedData.txt output file contains -1 values for miRNAs that were below the 0.5 intensity threshold in the 'tgsMicroRna' function, when half=TRUE.
>
> These -1 values are subsequently used in the analysis of differential genes (limma), which can (in my opinion) lead to false positive results.
> E.g. imagine a situation where the intensities for a miRNA of 2 control samples were below the detection limit of the scanner (noise) and therefore end up with a value of -1.
> For the 2 treated samples however the intensities were higher (1.395 and 1.147 respectively).
> This would generate a logFC of 2.271 and most likely a significant p-value. As a result, this miRNA would be selected as differentially expressed, whilst actually not being measured in 2 of the 4 samples.

I think I'm somewhat confused ... isn't the scenario you are
describing -- a miRNA is not detected in the control arrays, but
detected in the (presumably the "treatment" arrays) -- the definition
of differential expression?

Also, have you checked to see if this scenario you are imagining is
actually happening?

-steve

-- 
Steve Lianoglou
Computational Biologist
Genentech



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