no problems Andrew
-- apologies, I meant to reply all to keep this on the forum

Jim's recent response is accurate as well, but I have seen situations  
where large numbers of bad arrays pollute the remaining good arrays.  
it is perhaps unclear whether 2 or 3 out of 15 will affect your results.

in any case, I always re-normalise after removing poor quality arrays,  
i think it's safer that way (& easier for someone to repeat your  
analyses at a later date).

cheers,
Mark

On 30/08/2010, at 11:00 PM, Andrew Einhorn wrote:

> Apologies, I have worked the sub-setting thing out It actually  
> subsets fine the way I was doing it, don't know why the error was  
> coming up (had to restart R).
>
> On Mon, Aug 30, 2010 at 2:15 PM, Andrew Einhorn <andreweinhorn@gmail.com 
> > wrote:
> Thanks Mark.  So now I've identified my bad slides, how do I make a  
> subset of my original GeneFeatureSet (oligo class) to remove the bad  
> samples?  I have 18 samples and want to remove 7,8 and 11.
>
> myFS <- read.celfiles("cel_files", full.names = TRUE)
> # insert code to make myNewFS that excludes 7,8,11
> results <- rma(myNewFS)
>
> I have tried:
>
> myNewFS <- myFS[,1:6,9,10,12:18]
> results <- rma(myNewFS)
>
> but it throws the following error:
>  "Error in function (classes, fdef, mtable)  :
>   unable to find an inherited method for function "probeNames", for  
> signature "GeneFeatureSet""
>
> Thanks again
>
> Andrew
>
>
>
> On Mon, Aug 30, 2010 at 1:29 PM, Mark Cowley  
> <m.cowley@garvan.org.au> wrote:
> Hi Andrew,
> If the bad arrays also look like outliers in a density plot of the  
> log2-PM probes, before normalisation, then yes, keeping those 2 bad  
> arrays in will pollute the signal from your other arrays -- due to  
> the quantile normalisation step in RMA.
>
> cheers,
> Mark
> On 30/08/2010, at 5:12 PM, Andrew Einhorn wrote:
>
>> I have a set of 15 human gene st arrays that I am normalising.  From
>> analysis of the raw data, I can see that two of the slides are of  
>> very poor
>> quality (signs of rna degradation, low pearson correlations etc).   
>> If I do
>> an rma normalisation and include these two slides, will they effect  
>> the
>> normalisation of the other slides.  In other words, is it necessary  
>> to
>> ignore these two slides in the rma step, or will including them  
>> make no
>> difference.
>>
>> 	
>> [[alternative HTML version deleted]]
>>
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>
>
>
> -----------------------------------------------------
> Mark Cowley, PhD
>
> Peter Wills Bioinformatics Centre
> Garvan Institute of Medical Research, Sydney, Australia
> -----------------------------------------------------
>
>
>


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