[BioC] OT: Question about affymetrix array analysis and cRNA amount.

Jeanette McClintick jnmcclin at iupui.edu
Mon Jan 14 17:32:53 CET 2008

The scaling factor won't take care of all of the problems (It will actually
cause some problems). We have successfully prepared 200ul hybridization
cocktails using 10ug or less of cRNA. Use 15ul if you have 15ug cRNA, 10 if
you have 10 or less. This helps to compensate. See McClintick, et al. BMC
Genomics 2003 for comparison of arrays using different amounts of cRNA for
hybridization. If you have much less than 10ug, you will probably still have
some problems. I wouldn't go any lower than 7ug. Check the % present and
scaling factor to see if they are within reason. (+/- 2Std. deviations).
Contact me directly if want to discuss this further. 

Jeanette McClintick, PhD 
Indiana University School of Medicine 
Center for Medical Genomics 
Indianapolis, IN 
jnmcclin at iupui.edu 

-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of IAIN GALLAGHER
Sent: Monday, January 14, 2008 10:43 AM
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] OT: Question about affymetrix array analysis and cRNA


Sorry about the off topic (not bioconductor) question but with so many
statisticians and microarray users on the list I hoped it would be a good
place to post.

I am new to microarray work and we have clinical samples we would like to
run on Affymetrix chips. The RNA looks good by various analysis but the
amount of cRNA from many of the samples is suboptimal. 

My question is this: can we compensate for using different amounts of cRNA
at the analysis stage e.g. using a scaling factor or other means? For
instance if one chip ran with 15ug cRNA and another with 7ug can this be
accomodated sensibly or would the comparison of these two chips be
essentially meaningless?

Thank you for any advice.


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