Hi Anbarasu.
Comments below.
> Hi Mark,
>
> Thanks for your suggestions. What I have tried so far is: I removed all
outliers CEL files from rawData and re-run the analysis. I was expecting
a
> slightly different intensity distributions of chips (due to quantile
normalization) but it seems I have
Hi Mark,
Thanks for your suggestions. What I have tried so far is: I removed all
outliers CEL files from rawData and re-run the analysis. I was expecting a
slightly different intensity distributions of chips (due to quantile
normalization) but it seems I have the same distributions that I got with
Hi Anbarasu.
No, you don't have to remove all the files. What you can do is use
extract() to extract the files that you are interested in, and create
a new AffymetrixCelSet and fit the probe level modesl only on those
samples. You do need to be careful though and I suggest you use
*tags
