[BioC] followup on reading RNA digestion plots

[Swati Ranade]

Thanks Naomi. Will try your suggestion, but I get the
point, the trends of the curves are more important
than the slopes alone.
--- Naomi Altman <naomi at stat.psu.edu> wrote:
> Looking at the plot, I would not take the slopes too
> seriously!
> 
> I only eliminate an array if it appears to be
> dramatically different from 
> the others.  Your arrays vary (which is expected)
> but I do not see any 
> outlying array.
> 
> I suppose you could do a formal test, but I wouldn't
> bother.  To do the 
> test, you would probably want to use a
> semiparametric model of the form
> 
> curve(i) = m(i) + s(x)
> 
> where s(x) is the mean curve and m(i) is a random
> array effect.  Once you 
> fit the model, you could test the goodness of fit of
> each curve to the 
> model, adjust for multiple comparisons, and reject
> any significant 
> curves.  Sorry, I do not have a reference for this.
> 
> --Naomi
> 
> At 08:35 AM 3/28/2005, Swati Ranade wrote:
> 
> >   Hello,
> >
> >  A while ago I had posted a question about
> amplified>
> >RNA experiment and  guidelines one should follow
> >during data analysis and Dr. Gentleman had
> suggested
> >that RNA digestion plot will be a good indicator
> for
> >deciding which samples should be used in data
> analysis
> >as it is important to comapre likes. For my
> >experiments,I think prima facie the plots look
> quite a
> >bit similar but since I am new to this area
> >I cannot estimate what should be range of
> difference
> >in slopes that one should tolerate while choosing
> the
> >comparable profiles. To give an idea of what I am
> >seeing I am attaching a postscript image and giving
> >the slopes at the bottom of this email. I will be
> >extremely obliged if somebody could provide me
> >further guidance so that I know I am on the right
> >track. Please let me know if I need to provide more
> >than the following information?
> >
> >  Thanks,
> >
> >  Swati
> >
> >Here is the data: (I think sample # 8 seems to have
> >a slope that is different fro the rest!! Should it
> be
> >eliminated or one should observe the trend of the
> >graph?)
> >$slope
> >  [1] 1.6329065 1.5580935 1.5640235 0.9613637
> >  1.2156617 1.2004132 1.4831510
> >  [8] 0.3772531 1.6212330 1.2952673 1.2148458
> >  1.6020575 1.8564214 1.0944649
> >
> >
> >
> >
> >__________________________________________________
> >
> >
> >
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> 
> Naomi S. Altman                               
> 814-865-3791 (voice)
> Associate Professor
> Bioinformatics Consulting Center
> Dept. of Statistics                             
> 814-863-7114 (fax)
> Penn State University                        
> 814-865-1348 (Statistics)
> University Park, PA 16802-2111
> 
>