[BioC] followup on reading RNA digestion plots
Naomi Altman
naomi at stat.psu.edu
Mon Mar 28 16:53:13 CEST 2005
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
>
>
>
>
>__________________________________________________
>
>
>
>_______________________________________________
>Bioconductor mailing list
>Bioconductor at stat.math.ethz.ch
>https://stat.ethz.ch/mailman/listinfo/bioconductor
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
More information about the Bioconductor
mailing list