[BioC] QC - Illumina chip - Lumi Package

[Sean Davis]

On Thu, Apr 17, 2008 at 9:52 PM, Yogi Sundaravadanam
<yogi.sundaravadanam at agrf.org.au> wrote:
> Hi Sean,
>
>  Thanks,
>
>  It was just a Mouse 6-sample chip. Only one sample out of that is what I am interested in. Other 5 were used for some other experiment.
>
>  Is it worth looking at all the samples?

I think so, yes.  It will give you some comparison.  If your sample
does not appear to be an outlier in terms of intensity and controls,
that is useful information.  If it does appear to be an outlier, then
you will need to look into reasons for that.

Sean

>  -----Original Message-----
>  From: Sean Davis [mailto:sdavis2 at mail.nih.gov]
>  Sent: Friday, April 18, 2008 11:45 AM
>  To: Yogi Sundaravadanam
>  Cc: bioconductor
>  Subject: Re: [BioC] QC - Illumina chip - Lumi Package
>
>  On Thu, Apr 17, 2008 at 8:05 PM, Yogi Sundaravadanam
>  <yogi.sundaravadanam at agrf.org.au> wrote:
>  > Hi All
>  >
>  >
>  >
>  >  We have designed a 16 samples experiment. However, one sample only has
>  >  so far been amplified and hybridised to a mouse Illimina chip to see
>  >  whether or not there would be enough material to generate reliable
>  >  results from all the others not yet processed.
>  Hi, Yogi.
>
>  What Illumina chip were you using that had only one sample on it, just
>  out of curiosity?  Or, do you mean that you had a 6-sample chip and
>  ran only one sample on it?  Or did you run six samples but are only
>  interested in one?
>
>  If you are in the last situation, I would get the data from all six
>  samples on the chip.  That will be potentially helpful.
>
>  Sean
>
>  >  Looking at the lumi package, there isn't much I could do with just one
>  >  sample. Are there QC methods that would enable us to say that the chip
>  >  actually produces reliable results, please?
>  >
>  >  > summary(data, "QC")
>  >
>  >  Data dimension:  46628 genes x 1 samples
>  >
>  >
>  >
>  >  Summary of Samples:
>  >
>  >                         5-has a
>  >
>  >  mean                     5.3240
>  >
>  >  standard deviation       1.1740
>  >
>  >  detection rate(0.01)     0.2206
>  >
>  >  distance to sample mean  0.0000
>  >
>  >
>  >
>  >
>  >
>  >  With respect to Detection rate, what would be considered normal and
>  >  good?
>  >
>  >
>  >
>  >  Thanks heaps
>  >
>  >
>  >
>  >  Yogi
>  >
>  >
>  >
>  >
>  >
>  >         [[alternative HTML version deleted]]
>  >
>  >
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