[BioC] different normalized results using oneChannelGUI, and oligo packages
Javier Pérez Florido
jpflorido at gmail.com
Mon Nov 16 17:46:22 CET 2009
Dear Benilton,
Sorry, you were right. I was too confident (I had a look at the first
hundred of rows and the probesets were the same BUT they were misaligned
around the probeset number 4000 towards). I aligned the rows manually
and the mean relative error using all.equal() was 0.001885846.
Therefore, APT tools and oligo produce the expression set in different
order regarding the probesets.
Apologise again for this and thanks again for your kindly help.
Kind regards,
Javier
Benilton Carvalho escribió:
> 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:
>> o 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
>> o 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:
>> o 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
>> o 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:
>> o 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
>> o 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 at 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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