[BioC] xps Error in exonLevel(exonlevel, chiptype) : invalid argument ‘exonlevel’

[Dick Beyer]

Hi Christian,

Thanks for the update.  I was planning on figuring out what the probset difference was between xps and ExpresionConsole, so thanks for saving me that effort.  I appreciate it.

Cheers,
Dick

*******************************************************************************
Richard P. Beyer, Ph.D.	University of Washington
Tel.:(206) 616 7378	Env. & Occ. Health Sci. , Box 354695
Fax: (206) 685 4696	4225 Roosevelt Way NE, # 100
 			Seattle, WA 98105-6099
http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html
http://staff.washington.edu/~dbeyer
*******************************************************************************

On Wed, 14 May 2008, cstrato wrote:

> Dear Dick
>
> After checking my old records I realized that I did indeed compare the output 
> of my package with the output from ExpressionConsole. Here is what I did:
>
> Since Affymetrix supplies a user-modifyable meta-probest file *.mps for 
> ExpressionConsole, which in your case will be "MoGene-1_0-st-v1.r3.mps", I 
> simply replaced the probeset_id and transcript_cluster_id columns with the 
> probest IDs I get from validData(). Running ExpressionConsole with this 
> modified meta-probeset file will show you that the results are almost 
> identical, with the difference due to ExpressionConsole using Sketch-Quantile 
> normalization.
>
> I hope this late reply is helpful for you.
>
> Best regards
> Christian
>
> Dick Beyer wrote:
>> Hi Christian,
>> 
>> Is there a choice of values to the agruments for rma that gets the same 
>> results as Affy Expression Console?  I notice that from Affy Expression 
>> Console I get an output with 35557 rows, but with either of these choices:
>> 
>> data.rma7 <- rma(data.laspada, 
>> "laspadaCMRapRMA7",tmpdir="",background="antigenomic",normalize=TRUE, 
>> verbose=TRUE,exonlevel="affx+core")
>> data.rma8 <- rma(data.laspada, 
>> "laspadaCMRapRMA8",tmpdir="",background="antigenomic",normalize=TRUE, 
>> verbose=TRUE,exonlevel="all")
>> 
>> then validData(data.rma7) or validData(data.rma8) gives me a matrix with 
>> just 28837 rows.
>> 
>> Thanks very much,
>> Dick
>> ******************************************************************************* 
>> Richard P. Beyer, Ph.D.    University of Washington
>> Tel.:(206) 616 7378    Env. & Occ. Health Sci. , Box 354695
>> Fax: (206) 685 4696    4225 Roosevelt Way NE, # 100
>>             Seattle, WA 98105-6099
>> http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html
>> http://staff.washington.edu/~dbeyer
>> ******************************************************************************* 
>> On Fri, 9 May 2008, cstrato wrote:
>> 
>>> Dear Dick
>>> 
>>> I am glad to hear that you could now run rma.
>>> 
>>> Please feel free to inform me about any potential problems, omissions in 
>>> the help file, or potential improvements.
>>> 
>>> Best regards
>>> Christian
>>> 
>>> 
>>> Dick Beyer wrote:
>>>> Hi Christian,
>>>> 
>>>> Thanks for your good help.  I'm a repeat offender when it comes to not 
>>>> reading all the way through examples.  Thanks for your patience.
>>>> 
>>>> Using background="antigenomic" made my rma call work just fine.
>>>> 
>>>> Cheers,
>>>> Dick
>>>> ******************************************************************************* 
>>>> Richard P. Beyer, Ph.D.    University of Washington
>>>> Tel.:(206) 616 7378    Env. & Occ. Health Sci. , Box 354695
>>>> Fax: (206) 685 4696    4225 Roosevelt Way NE, # 100
>>>>             Seattle, WA 98105-6099
>>>> http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html
>>>> http://staff.washington.edu/~dbeyer
>>>> ******************************************************************************* 
>>>> On Fri, 9 May 2008, cstrato wrote:
>>>> 
>>>>> Dear Dick
>>>>> 
>>>>> Thank you for your tests, which make it clear to me that I need to 
>>>>> improve the help files.
>>>>> 
>>>>> Since MoGene arrays as well as exon arrays have no MM, you need to 
>>>>> set: background="antigenomic"
>>>>> 
>>>>> Please have a look at directory "xps/examples" which contains files 
>>>>> "script4xps.R" and "script4exon.R":
>>>>> In these scripts I give numerous examples which you can copy/paste and 
>>>>> adapt to your needs, especially I describe how to use the Affymetrix 
>>>>> human tissue dataset with arrays HG-U133_Plus_2, HuGene-1_0-st-v1.r3 
>>>>> and HuEx-1_0-st-v2.r2.
>>>>> 
>>>>> For HuGene the rma example is as follows:
>>>>> data.rma <- 
>>>>> rma(data.genome,"HuGeneMixRMAMetacore",filedir=datdir,tmpdir="",
>>>>>                 background="antigenomic",normalize=T,exonlevel="metacore+affx")
>>>>> 
>>>>> Please let me know if these informations could help you solve your 
>>>>> problem.
>>>>> 
>>>>> Best regards
>>>>> Christian
>
>