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]]
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor@stat.math.ethz.ch
>>
https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives:
http://news.gmane.org/gmane.science.biology.informatics.conductor
>
>
>
> -----------------------------------------------------
> Mark Cowley, PhD
>
> Peter Wills Bioinformatics Centre
> Garvan Institute of Medical Research, Sydney, Australia
> -----------------------------------------------------
>
>
>
[[alternative HTML version deleted]]
