[BioC] maanova background correction

[kfbargad at lg.ehu.es]

I agree that subtracting background can add variability to your 
dataset, but I think that if you don´t subtract it you risk having 
spots with a signal value composed of its real signal value plus a 
high background signal value. What do you think about prefiltering for 
those spots with an ubnormal high background value and then doing your 
analysis? Could this be an option?

David

> I think you have come across a relatively contentious issue, and I 
doubt
> you will be able to get a consensus about background subtraction.
> Additionally, each software/scanner uses a different method of
> estimating background, so the usefulness of the background is largely
> dependent on how it was estimated.
> 
> Personally, I look at background subtraction the same way I look at 
the
> MM probes on an Affy chip. I am sure there is a reasonable way to use
> these data, but I am not too sure that simply subtracting background
> from foreground is a good idea. For instance, background is usually
> estimated from portions of the slide that are blocked with something
> other than cDNA. Anybody that has ever looked at a slide with 
negative
> control cDNA spots can tell you that the intensity of the negative
> control is almost always much smaller than background. In my opinion,
> this indicates that the estimated background almost always 
overestimates
> true background.
> 
> In addition, variability is additive, so if you subtract background
> from foreground, you are adding the variability of your background
> estimate to your new foreground estimate. Considering the inherent
> variability of microarray data, this cannot be considered a good 
thing.
> 
> On the other hand, if you don't subtract background (or some ad hoc
> estimate thereof), your data will be (possibly) upwardly biased.
> 
> So here is what I do; I simply use the raw signal and accept that the
> data may be biased. This is certainly not the ideal situation, but I
> think it is a reasonable trade off of bias for (hopefully) better
> precision.
> 
> HTH,
> 
> Jim
> 
> 
> 
> James W. MacDonald
> UMCCC Microarray Core Facility
> 1500 E. Medical Center Drive
> 7410 CCGC
> Ann Arbor MI 48109
> 734-647-5623
> 
> >>> "Brendan M. Heavey" <bmheavey at buffalo.edu> 06/24/03 02:56PM >>>
> Hello-
> 
> I am using MAANOVA to analyze cDNA chips.  Does anybody know how to 
> deal with background spot intensity?
> 
> Right now, I have about 4000 genes on an array, each spotted 3 
times. 
> 
> I can input the raw signal strength for each of the 12,000 spots and 
> run analysis on those.
> 
> I would like to subtract background intensity from each of the 
spots, 
> but this leads to negative values in some spots (that haven't 
> hybridized).  Maanova seems to not like negatives or missing values, 
> which means I have to eliminate all 3 spots for each gene that 
produces
> 
> a single negative...which reduces my dataset to a pitiful number of 
> genes.
> 
> I've considered:
> 1). Replacing the missing/negative value with a number very close to 
> zero
> 2). Replacing the missing/negative value with the average of the 
other
> 
> two spots
> 3). Forgetting about background intensity completely and just using 
raw
> 
> signal strength
> 
> ...but none of them seem like the right thing to do
> 
> any ideas?
> 
> thanks in advance
> 
> Brendan Heavey
> Analyst Programmer
> Center for Research in Cardiovascular Medicine
> University at Buffalo
> 
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