[aroma.affymetrix] Re: FIRMAGene
Hi Ettore. Comments below. > I have the following question. In the "sup3.R" file the probe level > model fitting is realised using the instructions: > > plm <- RmaPlm(csNU) > fit(plm, verbose=verbose) > > where csNU is an object obtained after background correction, quantile > normalisation and conversion of the cdf to a "unique" version. The conversion to 'unique' is actually done both on the CDF and the data. This is simply to dance around the fact that a handful of probes are used in multiple probesets. > I suppose that this approach should enable the exon-level analysis of > the Gene 1.0 data, as required by FIRMAGene. However I don't > understand where is the difference since the methods are the same as > in the gene-level analysis of such data. I'm actually not sure what it is you are asking here. Indeed, the methodology of FIRMAGene operates on the results (specifically, the residuals) of your standard RMA probe level model. This is, however, quite different to the standard DE analysis, if that is what you mean by "gene-level analysis". Hope that helps. Cheers, Mark > > Thanks, > > > Ettore M. > > > On May 29, 3:16 pm, rhizomorph wrote: >> I have the same question as Ettore. I installed the aroma.affymetrix >> package (and all supporting packages), but nowhere can I find a source >> to download and install the FIRMAGene package that the "SUP3.R" script >> clearly calls for. >> >> Rhizomorph. >> >> On May 29, 3:15 am, ettore mosca wrote: >> >> > Dear aroma.affymetrix developers, >> >> > I'm very interested in using Gene 1.0 ST platform for alternative >> > splicing. I read in your paper "Differential splicing using >> > whole-transcript microarrays" that FIRMAGene "is freely available as R >> > package" but I can not load the library following the instruction in >> the >> > third additional file "sup3.r" (I installed and loaded >> aroma.affymetrix >> > successfully) >> >> > How do I install and load FIRMAGene library? >> >> > Thanks, >> >> > Ettore M. >> >> > -- >> > Ettore M. >> >> >http://www.ettoremosca.it > > > --~--~-~--~~~---~--~~ When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe from this group, send email to aroma-affymetrix-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/aroma-affymetrix?hl=en -~--~~~~--~~--~--~---
[aroma.affymetrix] Re: defining cell files
library("aroma.affymetrix")
for loading the package.
/H
On Thu, Jun 4, 2009 at 8:45 AM, Myriam Peyrard wrote:
>
> Ok, thank you so much, Pierre. I shall try and if not working, get back
> to you again.
> The output I gave you was the one I got but, finally (my second day
> using R and Aroma Affymetrix, as I sai, a brand new beginner!!!), at the
> end of the day, I realized that I had forgotten to open the aroma
> library and so on, at the beginning of my R session. So I guess the
> error was there and that is also why the output was the one I got.
>
> I hope I have better "luck" tomorrow!!!
> Myriam
>
> - Original Message -
> From: Pierre Neuvial
> Date: Thursday, June 4, 2009 3:41 pm
> Subject: [aroma.affymetrix] Re: defining cell files
> To: aroma-affymetrix@googlegroups.com
>
>>
>> OK, I meant the other way round: the name of the folder should be
>>
>> rawData/CLP/GenomeWideSNP_6
>>
>> not
>>
>> rawData/CLP/GenomeWideSNP_6.0
>>
>> Best,
>>
>> Pierre.
>>
>> On Thu, Jun 4, 2009 at 6:36 AM, Pierre Neuvial
>> wrote:
>> > Hi Myriam,
>> >
>> > On Thu, Jun 4, 2009 at 4:38 AM, Myriam wrote:
>> >>
>> >> Hi,
>> >>
>> >> I have done (and seems OK, no error message) the low level
>> analysis of
>> >> the GenomeWideSNP_6.0 for preparing the analysis of my Affymetrix
>> >> results in 50 samples.
>> >> However, I cannot get through the steps of defining the CEL
>> files set.
>> >> I have put all the CEL files in rawData/CLP/GenomeWideSNP_6.0
>> folder.>> How should I define the set of CEL files to be analysed
>> and which are
>> >> contained in that subfolder?
>> >> Tried command:
>> >> cs <- AffymetrixCelSet$byName("CLP", cdf=cdf)
>> >> but error: AffymetrixCelSet not found
>> >
>> > The name of the folder containing the CEL files should match the
>> name> of the chip type exactly. In your case it should be
>> >
>> > rawData/CLP/GenomeWideSNP_6.0
>> >
>> > not
>> >
>> > rawData/CLP/GenomeWideSNP_6
>> >
>> > Does this work now ?
>> >
>> > For future posts: it's better to give the complete R output; In your
>> > case aroma.affymetrix probably reports something like:
>> >
>> > Cannot create AffymetrixCelSet. *No such directory:
>> CLP/GenomeWideSNP_6*>
>> > which tells you (and us) where the problem comes from.
>> >
>> > Best,
>> >
>> > Pierre
>> >
>> >>
>> >> I am a bit lost, as a beginner. Sorry to bother but hopefully
>> one of
>> >> you can help me?
>> >>
>> >> Thanks in advance,
>> >> Myriam
>> >>
>> >> >>
>> >>
>> >
>>
>> >
>>
>
> >
>
--~--~-~--~~~---~--~~
When reporting problems on aroma.affymetrix, make sure 1) to run the latest
version of the package, 2) to report the output of sessionInfo() and
traceback(), and 3) to post a complete code example.
You received this message because you are subscribed to the Google Groups
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[aroma.affymetrix] Re: defining cell files
Ok, thank you so much, Pierre. I shall try and if not working, get back
to you again.
The output I gave you was the one I got but, finally (my second day
using R and Aroma Affymetrix, as I sai, a brand new beginner!!!), at the
end of the day, I realized that I had forgotten to open the aroma
library and so on, at the beginning of my R session. So I guess the
error was there and that is also why the output was the one I got.
I hope I have better "luck" tomorrow!!!
Myriam
- Original Message -
From: Pierre Neuvial
Date: Thursday, June 4, 2009 3:41 pm
Subject: [aroma.affymetrix] Re: defining cell files
To: aroma-affymetrix@googlegroups.com
>
> OK, I meant the other way round: the name of the folder should be
>
> rawData/CLP/GenomeWideSNP_6
>
> not
>
> rawData/CLP/GenomeWideSNP_6.0
>
> Best,
>
> Pierre.
>
> On Thu, Jun 4, 2009 at 6:36 AM, Pierre Neuvial
> wrote:
> > Hi Myriam,
> >
> > On Thu, Jun 4, 2009 at 4:38 AM, Myriam wrote:
> >>
> >> Hi,
> >>
> >> I have done (and seems OK, no error message) the low level
> analysis of
> >> the GenomeWideSNP_6.0 for preparing the analysis of my Affymetrix
> >> results in 50 samples.
> >> However, I cannot get through the steps of defining the CEL
> files set.
> >> I have put all the CEL files in rawData/CLP/GenomeWideSNP_6.0
> folder.>> How should I define the set of CEL files to be analysed
> and which are
> >> contained in that subfolder?
> >> Tried command:
> >> cs <- AffymetrixCelSet$byName("CLP", cdf=cdf)
> >> but error: AffymetrixCelSet not found
> >
> > The name of the folder containing the CEL files should match the
> name> of the chip type exactly. In your case it should be
> >
> > rawData/CLP/GenomeWideSNP_6.0
> >
> > not
> >
> > rawData/CLP/GenomeWideSNP_6
> >
> > Does this work now ?
> >
> > For future posts: it's better to give the complete R output; In your
> > case aroma.affymetrix probably reports something like:
> >
> > Cannot create AffymetrixCelSet. *No such directory:
> CLP/GenomeWideSNP_6*>
> > which tells you (and us) where the problem comes from.
> >
> > Best,
> >
> > Pierre
> >
> >>
> >> I am a bit lost, as a beginner. Sorry to bother but hopefully
> one of
> >> you can help me?
> >>
> >> Thanks in advance,
> >> Myriam
> >>
> >> >>
> >>
> >
>
> >
>
--~--~-~--~~~---~--~~
When reporting problems on aroma.affymetrix, make sure 1) to run the latest
version of the package, 2) to report the output of sessionInfo() and
traceback(), and 3) to post a complete code example.
You received this message because you are subscribed to the Google Groups
"aroma.affymetrix" group.
To post to this group, send email to aroma-affymetrix@googlegroups.com
To unsubscribe from this group, send email to
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For more options, visit this group at
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-~--~~~~--~~--~--~---
[aroma.affymetrix] Re: FIRMAGene
I have the following question. In the "sup3.R" file the probe level model fitting is realised using the instructions: plm <- RmaPlm(csNU) fit(plm, verbose=verbose) where csNU is an object obtained after background correction, quantile normalisation and conversion of the cdf to a "unique" version. I suppose that this approach should enable the exon-level analysis of the Gene 1.0 data, as required by FIRMAGene. However I don't understand where is the difference since the methods are the same as in the gene-level analysis of such data. Thanks, Ettore M. On May 29, 3:16 pm, rhizomorph wrote: > I have the same question as Ettore. I installed the aroma.affymetrix > package (and all supporting packages), but nowhere can I find a source > to download and install the FIRMAGene package that the "SUP3.R" script > clearly calls for. > > Rhizomorph. > > On May 29, 3:15 am, ettore mosca wrote: > > > Dear aroma.affymetrix developers, > > > I'm very interested in using Gene 1.0 ST platform for alternative > > splicing. I read in your paper "Differential splicing using > > whole-transcript microarrays" that FIRMAGene "is freely available as R > > package" but I can not load the library following the instruction in the > > third additional file "sup3.r" (I installed and loaded aroma.affymetrix > > successfully) > > > How do I install and load FIRMAGene library? > > > Thanks, > > > Ettore M. > > > -- > > Ettore M. > > >http://www.ettoremosca.it --~--~-~--~~~---~--~~ When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe from this group, send email to aroma-affymetrix-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/aroma-affymetrix?hl=en -~--~~~~--~~--~--~---
[aroma.affymetrix] Re: defining cell files
OK, I meant the other way round: the name of the folder should be
rawData/CLP/GenomeWideSNP_6
not
rawData/CLP/GenomeWideSNP_6.0
Best,
Pierre.
On Thu, Jun 4, 2009 at 6:36 AM, Pierre Neuvial wrote:
> Hi Myriam,
>
> On Thu, Jun 4, 2009 at 4:38 AM, Myriam wrote:
>>
>> Hi,
>>
>> I have done (and seems OK, no error message) the low level analysis of
>> the GenomeWideSNP_6.0 for preparing the analysis of my Affymetrix
>> results in 50 samples.
>> However, I cannot get through the steps of defining the CEL files set.
>> I have put all the CEL files in rawData/CLP/GenomeWideSNP_6.0 folder.
>> How should I define the set of CEL files to be analysed and which are
>> contained in that subfolder?
>> Tried command:
>> cs <- AffymetrixCelSet$byName("CLP", cdf=cdf)
>> but error: AffymetrixCelSet not found
>
> The name of the folder containing the CEL files should match the name
> of the chip type exactly. In your case it should be
>
> rawData/CLP/GenomeWideSNP_6.0
>
> not
>
> rawData/CLP/GenomeWideSNP_6
>
> Does this work now ?
>
> For future posts: it's better to give the complete R output; In your
> case aroma.affymetrix probably reports something like:
>
> Cannot create AffymetrixCelSet. *No such directory: CLP/GenomeWideSNP_6*
>
> which tells you (and us) where the problem comes from.
>
> Best,
>
> Pierre
>
>>
>> I am a bit lost, as a beginner. Sorry to bother but hopefully one of
>> you can help me?
>>
>> Thanks in advance,
>> Myriam
>>
>> >>
>>
>
--~--~-~--~~~---~--~~
When reporting problems on aroma.affymetrix, make sure 1) to run the latest
version of the package, 2) to report the output of sessionInfo() and
traceback(), and 3) to post a complete code example.
You received this message because you are subscribed to the Google Groups
"aroma.affymetrix" group.
To post to this group, send email to aroma-affymetrix@googlegroups.com
To unsubscribe from this group, send email to
aroma-affymetrix-unsubscr...@googlegroups.com
For more options, visit this group at
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-~--~~~~--~~--~--~---
[aroma.affymetrix] Re: defining cell files
Hi Myriam,
On Thu, Jun 4, 2009 at 4:38 AM, Myriam wrote:
>
> Hi,
>
> I have done (and seems OK, no error message) the low level analysis of
> the GenomeWideSNP_6.0 for preparing the analysis of my Affymetrix
> results in 50 samples.
> However, I cannot get through the steps of defining the CEL files set.
> I have put all the CEL files in rawData/CLP/GenomeWideSNP_6.0 folder.
> How should I define the set of CEL files to be analysed and which are
> contained in that subfolder?
> Tried command:
> cs <- AffymetrixCelSet$byName("CLP", cdf=cdf)
> but error: AffymetrixCelSet not found
The name of the folder containing the CEL files should match the name
of the chip type exactly. In your case it should be
rawData/CLP/GenomeWideSNP_6.0
not
rawData/CLP/GenomeWideSNP_6
Does this work now ?
For future posts: it's better to give the complete R output; In your
case aroma.affymetrix probably reports something like:
Cannot create AffymetrixCelSet. *No such directory: CLP/GenomeWideSNP_6*
which tells you (and us) where the problem comes from.
Best,
Pierre
>
> I am a bit lost, as a beginner. Sorry to bother but hopefully one of
> you can help me?
>
> Thanks in advance,
> Myriam
>
> >
>
--~--~-~--~~~---~--~~
When reporting problems on aroma.affymetrix, make sure 1) to run the latest
version of the package, 2) to report the output of sessionInfo() and
traceback(), and 3) to post a complete code example.
You received this message because you are subscribed to the Google Groups
"aroma.affymetrix" group.
To post to this group, send email to aroma-affymetrix@googlegroups.com
To unsubscribe from this group, send email to
aroma-affymetrix-unsubscr...@googlegroups.com
For more options, visit this group at
http://groups.google.com/group/aroma-affymetrix?hl=en
-~--~~~~--~~--~--~---
[aroma.affymetrix] defining cell files
Hi,
I have done (and seems OK, no error message) the low level analysis of
the GenomeWideSNP_6.0 for preparing the analysis of my Affymetrix
results in 50 samples.
However, I cannot get through the steps of defining the CEL files set.
I have put all the CEL files in rawData/CLP/GenomeWideSNP_6.0 folder.
How should I define the set of CEL files to be analysed and which are
contained in that subfolder?
Tried command:
cs <- AffymetrixCelSet$byName("CLP", cdf=cdf)
but error: AffymetrixCelSet not found
I am a bit lost, as a beginner. Sorry to bother but hopefully one of
you can help me?
Thanks in advance,
Myriam
--~--~-~--~~~---~--~~
When reporting problems on aroma.affymetrix, make sure 1) to run the latest
version of the package, 2) to report the output of sessionInfo() and
traceback(), and 3) to post a complete code example.
You received this message because you are subscribed to the Google Groups
"aroma.affymetrix" group.
To post to this group, send email to aroma-affymetrix@googlegroups.com
To unsubscribe from this group, send email to
aroma-affymetrix-unsubscr...@googlegroups.com
For more options, visit this group at
http://groups.google.com/group/aroma-affymetrix?hl=en
-~--~~~~--~~--~--~---
