[BioC] Is it recommended to remove control probes for Agilent type data

[Yong Li]

Dear Ketaki,

it is not good to remove the controls probes before normalization. In
normalization step all the data points on the array should be
considered. Removing control probes and possible other filtering
should be done after normalization, before finding differentially
expressed genes.

Best regards,
Yong

On Mon, Jul 16, 2012 at 3:46 PM, Ketaki <bhide at purdue.edu> wrote:
>
> I have Agilent 2 color data with 8635 probes, however both negative and positive
> control probes comprise of 544 probes. If I remove control probes during
> normalization I tend to get more differentially expressed probes as compared to
> keeping the control probes suring normalization. Please advice me whether it is
> recommended to remove control probes while normalization or not?
>
> Summary of results
> i)Using control probes while normalization
> Upregulated probes 23
> Downregulated probes 58
>
> ii)Not using control probes while normalization
> Upregulated probes 105
> Downregualted probes 145
>
> Regards
> Ketaki
>
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