[BioC] Deciding on a cut off after QC

[Gordon K Smyth]

> Date: Sun, 15 May 2005 21:34:18 -0700 (PDT)
> From: Ankit Pal <pal_ankit2000 at yahoo.com>
> Subject: [BioC] Deciding on a cut off after QC
> To: bioconductor at stat.math.ethz.ch
>
> Dear All,
> I'm using LIMMA to analyse a set of GPR files.
> I used the weight fuction to apply QC parameter
> threshold values recommended by Genepix.
> The code for the same is
>
>>myfun <- function(x,threshold=55){
> + okred <- abs(x[,"% > B635+2SD"]) < threshold
> + okgreen <- abs(x[,"% > B532+2SD"]) < threshold
> + as.numeric(okgreen & okred)
> }
>
>  On completion of the analysis, all the spots showed
> up in the results file inspite of being flagged off. I
> understand that on being flagged off by limma (wt =
> 0), the spots are not considered for further analysis.
> Is there any way they can be excluded from the final
> result file.

What result file?

> Also, if I get an output of all the spots (38000 in my
> case) how do I decide on a cut off. Do I use the rank
> or something else?

What output?

Gordon

> Waiting eagerly for a reply,
> thank you,
> -Ankit