[BioC] RNA digestion plots

Tan, MinHan MinHan.Tan at vai.org
Thu Nov 20 18:15:25 MET 2003


I recall a post from the author of the RNA degradation plot function
that stated that the function was optimised for the HGU95 chips, not for
the HGU 133 chips, resulting in high 3'/5' ratios in the latter. 

As to why that should be the case, I confess that I do not know. 

I agree that a trend deviating outside the plots is more important. 
 
Regards,
Min-Han Tan

-----Original Message-----
From: Lawrence Paul Petalidis [mailto:lpp22 at cam.ac.uk] 
Sent: Thursday, November 20, 2003 6:03 AM
To: William Kenworthy; BioConductor List
Subject: RE: [BioC] RNA digestion plots


Hi William
The RNA plots on your site look great to me. I routinely work with
tumour clinical RNA and the slopes are significantly larger than yours
even if the quality of starting RNA appears to be good. You see, RNA
quality control relies heavily on ribosomal RNA quality (peaks).
However, I have had samples with great ribosomal peaks that actually
produce RNAdeg plots with a significant slope 5' to 3'. Its the state of
the mRNA that counts and that seems to be more sensitive to degradation
than the ribosomal one. I would be very happy working with the ones you
show on your site.

With kind regards, Lawrence

______________________________
Lawrence Paul Petalidis
Ph.D. Candidate

University of Cambridge
Department of Pathology
______________________________

-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch]On Behalf Of William
Kenworthy
Sent: 20 November 2003 07:22
To: BioConductor List
Subject: Re: [BioC] RNA digestion plots


RNA plots are something I have also been looking at, but all the
datasets I have access to can be characterised as "good".  Can anyone
supply a (anonymous?) "cel" file of any persuasion that is known to have
been used with degraded RNA?  On larger arrays, I do see a slight slope,
but not any "rolloff" which I think would represent degradation.

At the present time, I add a "typical" CELfile from another project that
seems good and adding that to the current affybatch and running the
plots.  Currently, they track very well across projects (especially if
normalised) - so a sample "bad one" would be nice just to see what it
looks like!

I have put four plots up at "http://wdk.dyndns.org/rna/rnadeg.html".
The red and black traces represent samples that I was informed "might"
have been questionable, but they did pass affy's check criteria, the
green trace is from an experiment that was considered good.

BillK


On Thu, 2003-11-20 at 13:27, Kevin Dawson wrote:
> Does any one know when to take the RNA digestion plots seriously. On 
> hgu133a arrays, these plots always seem to incline from 5' to 3'. Is 
> there a certain slope value that sets the good and bad apart?
>
> Thank you
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch 
> https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor

_______________________________________________
Bioconductor mailing list
Bioconductor at stat.math.ethz.ch
https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor

_______________________________________________
Bioconductor mailing list
Bioconductor at stat.math.ethz.ch
https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential information.  Any unauthorized review, use, disclosure or distribution is prohibited.  If you are not the intended recipient(s) please contact the sender by reply email and destroy all copies of the original message.  Thank you.



More information about the Bioconductor mailing list