Are you sure the probesets are in the same order?

Instead of (A-B)/N, you could use all.equal(A,B), which will also  
assess dimnames, especially important in this case (because you'll be  
able to notice if the probesets are alligned).

When I first wrote the code I did this comparison myself and the  
relative difference was something like 1e-4.

So, my guess: probesets are misaligned.

Best,
b

On Nov 16, 2009, at 8:00 AM, Javier Pérez Florido wrote:

> Dear Benilton and Raffaele,
> I've tried what you suggested and I got the following results:
> Comparison between rma and rma-sketch using APT tools:
> apt-probeset-summarize -a rma -p Hugene-1_0-st-v1.r3.pgf -c  
> Hugene-1_0-st-v1.r3.clf -m Hugene-1_0-st-v1.r3.mps -o rma --cel- 
> files cel_list.txt
> apt-probeset-summarize -a rma-sketch -p Hugene-1_0-st-v1.r3.pgf -c  
> Hugene-1_0-st-v1.r3.clf -m Hugene-1_0-st-v1.r3.mps -o rma-sketch -- 
> cel-files cel_list.txt
> The error given by abs(exprs(rma)-exprs(rma-sketch)) / num_points is  
> 1.4147e-004
> Comparison between rma using APT tools and rma using oligo:
> apt-probeset-summarize -a rma -p Hugene-1_0-st-v1.r3.pgf -c  
> Hugene-1_0-st-v1.r3.clf -m Hugene-1_0-st-v1.r3.mps -o rma --cel- 
> files cel_list.txt
> OligoEset<-rma(OligoRaw,target="core")
> The error given by abs(exprs(rma)-exprs(OligoEset)) / num_points is  
> 1.8915
> Comparison between rma-sketch using APT tools and rma using oligo:
> apt-probeset-summarize -a rma-sketch -p Hugene-1_0-st-v1.r3.pgf -c  
> Hugene-1_0-st-v1.r3.clf -m Hugene-1_0-st-v1.r3.mps -o rma --cel- 
> files cel_list.txt
> OligoEset<-rma(OligoRaw,target="core")
> The mean error given by abs(exprs(rma-sketch)-exprs(OligoEset)) /  
> num_points is 1.8915
> Surprisingly, the difference between APT tools and oligo are quite  
> high (you can notice it when having a look at the normalized data).
> Is there anything wrong above?
> Thanks,
> Javier
>
>
>
> Benilton Carvalho escribió:
>>
>> Thanks for the heads up, Raffaele.
>>
>> My suggestion was Javier to try "-a rma" manually, instead of "-a  
>> rma-sketch" (which appears to be what oneChannelGUI uses - at least  
>> that's what I saw when skimmed the source ).
>>
>> cheers,
>>
>> b
>>
>> On Nov 12, 2009, at 6:32 AM, rcaloger wrote:
>>
>>> Hi,
>>> dear Benilton,
>>> you are right oneChannelGUI uses sketch-quantile. APT-tools are  
>>> used by oneChannelGUI to calculate intensities.
>>> Actually oneChannelGUI uses a graphical interface to execute
>>> apt-probeset-summarize -a rma -p PGFFILE.pgf -c CLFFILE.clf  -m   
>>> MPSFILE.mps -out rmasketch *.cel
>>> cheers
>>> Raffaele
>>>
>>>
>>>> Javier,
>>>
>>>> my knowledge on the oneChannelGUI is pretty limited, but it seems  
>>>> to
>>>> me that it does either rma-sketch or iter-plier.
>>>
>>>> oligo will do the "regular" rma, ie. no sketch normalization.  
>>>> Now, if
>>>> you could download APT and run it yourself (I'm not sure how it is
>>>> packaged in oneChannel), you could try the following:
>>>
>>>> apt-probeset-summarize -a rma -p PGFFILE.pgf -c CLFFILE.clf  -m
>>> MPSFILE.mps -out rmasketch *.cel
>>>
>>>> And you may get more similar results... I'm not saying they'll be
>>>> identical, but when I implemented this for oligo the mean relative
>>>> difference between oligo and APT was something like 0.001.
>>>
>>> b
>>>
>>> On Nov 10, 2009, at 3:30 PM, Javier P?rez Florido wrote:
>>>
>>>
>>>>> Dear all,
>>>>> I have normalized a GeneChip Human Gene ST 1.0 dataset using oligo
>>>>> package and oneChannelGUI. I've checked that the log2 normalized
>>>>> values
>>>>> are different (not so different, but different). When applying  
>>>>> limma
>>>>> on
>>>>> them, the statistic values (p-value, M, B and statistic t) are  
>>>>> also
>>>>> different.
>>>>>
>>>>> I've read that oneChannelGUI uses APT tools to summarize data and,
>>>>> maybe, that is the point: they produce similar but different
>>>>> normalized
>>>>> values that have an effect in the final list of differentially
>>>>> expressed
>>>>> genes.
>>>>>
>>>>> For oligo, I've normalized using rma method and core as a target:
>>>>> OligoEset<-rma(OligoRaw,target="core")
>>>>> For oneChannelGUI, I've used the option "Load gene 1.0 ST arrays  
>>>>> from
>>>>> .CEL files."
>>>>>
>>>>> In both cases, the limma parameters are the same.
>>>>> So, I suspect the APT tools used by oneChannelGUI has influence  
>>>>> on the
>>>>> data. Is there a way to normalize the raw data in OneChannelGUI to
>>>>> select the subgroup (core) instead of using APT tools? I think  
>>>>> this is
>>>>> only available in Exon Arrays.
>>>>>
>>>>> Or may be I am wrong with these conclusions.
>>>>> Any tips?
>>>>> Thanks,
>>>>> Javier
>>>>>
>>>>
>>> -- 
>>>
>>> ----------------------------------------
>>> Prof. Raffaele A. Calogero
>>> Bioinformatics and Genomics Unit
>>> Dipartimento di Scienze Cliniche e Biologiche
>>> c/o Az. Ospedaliera S. Luigi
>>> Regione Gonzole 10, Orbassano
>>> 10043 Torino
>>> tel.   ++39 0116705417
>>> Lab.   ++39 0116705408
>>> Fax    ++39 0119038639
>>> Mobile ++39 3333827080
>>> email: raffaele.calogero@unito.it
>>>       raffaele[dot]calogero[at]gmail[dot]com
>>> www:   http://www.bioinformatica.unito.it
>>> Info: http://publicationslist.org/raffaele.calogero
>>>
>>
>>
>


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