[BioC] Bioconductor - hugene10stv1cdf not available

[James W. MacDonald]

Christoph Knapp wrote:
> Now I'm getting following error. This chip type gives me a headache
> and if I go on probably gastric ulcer to.

This is (again) something that has been asked and answered many times on 
this list. And it is a case study in what happens when one uses tools 
blindly without knowing what the tool is designed for.

A quick peek at the vignettes makes me think that this isn't explicitly 
spelled out, which is definitely a problem. However, before embarking on 
the analysis of some data, it is IMO very important to know at least a 
little bit about the underlying analysis methodology and what data you 
are working with (and that's on you).

The simpleaffy package is designed for the so-called 3'-biased arrays, 
which used a T7-oligo(dT) primer that binds to the poly-A tail of mRNA, 
in order to do the in vitro translation. Because of this, the resulting 
cDNA tends to be 3' biased, so it is a good idea to see how bad the bias 
is, which indicates how well (or poorly) the IVT step worked.

In addition, the 3'-biased arrays (almost) all have both PM and MM 
probes, which are both required for some of the quality control steps in 
the simpleaffy package.

The HuGene array does not use the T7-Oligo(dT) primer, instead, the IVT 
step uses random primers, so the concern over 3'-bias is negligible. In 
addition, the HuGene array is PM-only, so any quality control step that 
uses MAS5 or computes present/absent calls is not going to work.

Because of this, it doesn't make much sense to use the simpleaffy 
package to do quality control of the HuGene chip.

Best,

Jim


> 
> Error in setQCEnvironment(cdfn) :
>   Could not find array definition file ' hugene10stv1.r3cdf.qcdef '.
> Simpleaffy does not know the QC parameters for this array type.
> See the package vignette for details about how to specify QC
> parameters manually.
> Calls: qc -> qc -> qc.affy -> setQCEnvironment
> Execution halted
> 
> This happens in
> 
> QCReport(VFdata,file=paste(totalJobpath,"\\","AffyQCReport.pdf",sep=""))
> 
> It generates some of the report but not all.
> 
> I tried
> 
> setQCEnvironment(cleancdfname(cdfName(eset)))
> 
> as suggested in
> 
> http://127.0.0.1:25446/library/simpleaffy/html/setQCEnvironment.html
> 
> but that did not help.
> 
> Please help?
> 
> Christoph
> 
> On 20 April 2010 11:03, Sherri Christian <sherri at mun.ca> wrote:
>> Christoph,
>>
>> I do not have a lot of experience with Bioconductor but my experience is
>> that for some chips (ie. mouse4302), the information is retrieved
>> automatically but for the hugene10 chip it is not. My understanding is that
>> it is because of the syntax of the file that is suggested by the CEL file
>> (this is what I understood from the vignettes). If you want to set up for
>> other people then the best way is probably to set up text files (or TinnR
>> files) that have all the essential "start-up" commands on a "per chip"
>> basis. This is pretty much the limit of my knowledge!
>>
>> Sherri
>>
>> On 19-Apr-10, at 7:30 PM, Christoph Knapp wrote:
>>
>>> That works well, thanks a lot, but how I said in a previous email, my
>>> project is about writing an application which takes in many different
>>> cel files without throwing exceptions. Its about making life easier
>>> for people who know even less about that stuff than I do ;-). Thats
>>> why I need a way to setup R so that it works without problems in a
>>> standard way. Is there a possibility to retrieve information's from
>>> the cel files itself what the latest version of annotation package is
>>> it needs? Than I could just pass this information into the readAffy()
>>> command similar to the way you suggested.
>>>
>>> Sorry for being a pain and thanks for the help.
>>>
>>> Christoph
>>>
>>> On 19 April 2010 23:28, Sherri Christian <sherri at mun.ca> wrote:
>>>> sorry all, I forgot to change the name of the subject
>>>> S
>>>>
>>>> Begin forwarded message:
>>>>
>>>> From: Sherri Christian <sherri at mun.ca>
>>>> Date: April 19, 2010 8:53:25 AM NDT
>>>> To: bioconductor at stat.math.ethz.ch, mkna005 at aucklanduni.ac.nz
>>>> Cc: Sherri Christian <sherri at mun.ca>
>>>> Subject: Re: Bioconductor Digest, Vol 86, Issue 19
>>>> Hi Christoph,
>>>> First, install the package as suggested by Benilton - the name that you
>>>> tried was not correct
>>>>> biocLite("hugene10stv1.r3cdf")
>>>> Then load the library
>>>>> library("hugene10stv1.r3cdf")
>>>> Then read in your data
>>>>> data <- ReadAffy()  #will read in all CEL files in your working
>>>>> directory
>>>> Then tell Affy which cdf file it needs to use- because the name of the
>>>> CDF
>>>> file that Affy thinks it needs is NOT what you downloaded
>>>>> data at cdfName <- "hugene10stv1.r3cdf"
>>>> Now check your data to be sure that the correct cdf file was used
>>>>> data
>>>> good luck,
>>>> Sherri
>>>>
>>>> Date: Mon, 19 Apr 2010 01:51:17 +0100
>>>> From: Benilton Carvalho <beniltoncarvalho at gmail.com>
>>>> To: Christoph Knapp <mkna005 at aucklanduni.ac.nz>
>>>> Cc: bioconductor at stat.math.ethz.ch
>>>> Subject: Re: [BioC] Bioconductor - hugene10stv1cdf not available
>>>> Message-ID:
>>>> <v2se71a39ea1004181751p8be0629cnb483027cda4c1b95 at mail.gmail.com>
>>>> Content-Type: text/plain; charset=windows-1252
>>>> btw, if you want to use the affy package, I believe that the package:
>>>>
>>>> http://www.bioconductor.org/packages/release/data/annotation/html/hugene10stv1.r3cdf.html
>>>> should suffice (you will need to specify the name of the package to be
>>>> used though, check the docs for ReadAffy).
>>>> b
>>>> On Mon, Apr 19, 2010 at 1:48 AM, Benilton Carvalho
>>>> <beniltoncarvalho at gmail.com> wrote:
>>>>
>>>> Hi Christoph,
>>>> the way to do this with oligo is:
>>>> library(oligo)
>>>> rawData = read.celfiles(list.celfiles())
>>>> summaries1 = rma(rawData, target="probeset")
>>>> summaries2 = rma(rawData, target="core")
>>>> summaries1 will contain the rma summaries to the probeset defined in
>>>> the PGF file. summaries2 will contain the summaries for the
>>>> metaprobesets defined in the core.mps file.
>>>> AffyBatch objects are to be used with the affy package, so that's why
>>>> the pd.hugene package was of no use (b/c pd.hugene is to be used with
>>>> oligo).
>>>> hth,
>>>> b
>>>> On Mon, Apr 19, 2010 at 1:33 AM, Christoph Knapp
>>>> <mkna005 at aucklanduni.ac.nz> wrote:
>>>>
>>>> I forgot to mention that I tried that as well:
>>>>
>>>> ? ? biocLite("hugene10stv1cdf")
>>>>
>>>> Using R version 2.10.1, biocinstall version 2.5.10.
>>>> Installing Bioconductor version 2.5 packages:
>>>> [1] "hugene10stv1cdf"
>>>> Please wait...
>>>> Warning message:
>>>> In getDependencies(pkgs, dependencies, available, lib) :
>>>> ?package ?hugene10stv1cdf? is not available
>>>> Why is it not possible for me to install that package.
>>>> Thanks
>>>> Christoph
>>>> On 19 April 2010 12:13, Christoph Knapp <mkna005 at aucklanduni.ac.nz>
>>>> wrote:
>>>>
>>>> Sorry,
>>>> still no change
>>>> AffyBatch object
>>>> size of arrays=1050x1050 features (11 kb)
>>>> cdf=HuGene-1_0-st-v1 (??? affyids)
>>>> number of samples=7
>>>> Error in getCdfInfo(object) :
>>>> ?Could not obtain CDF environment, problems encountered:
>>>> Specified environment does not contain HuGene-1_0-st-v1
>>>> Library - package hugene10stv1cdf not installed
>>>> Bioconductor - hugene10stv1cdf not available
>>>> In addition: Warning message:
>>>> missing cdf environment! in show(AffyBatch)
>>>> Christoph
>>>> On 19 April 2010 11:51, Benilton Carvalho <beniltoncarvalho at gmail.com>
>>>> wrote:
>>>>
>>>> the pd.hugene package (which I'd expect you to download from BioC) is
>>>> to be used with the oligo package.
>>>> b
>>>> On Sun, Apr 18, 2010 at 11:51 PM, Christoph Knapp
>>>> <mkna005 at aucklanduni.ac.nz> wrote:
>>>>
>>>> Hi all,
>>>> I'm trying for quite some time to get an analysis started. I keep
>>>> getting this Error.
>>>> Error in getCdfInfo(object) :
>>>> ?Could not obtain CDF environment, problems encountered:
>>>> Specified environment does not contain HuGene-1_0-st-v1
>>>> Library - package hugene10stv1cdf not installed
>>>> Bioconductor - hugene10stv1cdf not available
>>>> Calls: rma ... .local -> indexProbes -> indexProbes -> .local ->
>>>> getCdfInfo
>>>> Execution halted
>>>> I installed all possible packages from there
>>>> http://www.bioconductor.org/docs/workflows/oligoarrays/
>>>> and even downloaded and installed that one
>>>> http://mbi00206.bio.med.uni-muenchen.de/free/pd.hugene.1.0.st.v1.zip)
>>>> still no change.
>>>> What am I missing?
>>>> It reads in the CEL files
>>>> VFdata=ReadAffy()
>>>> but when I look at the VFdata object it already says
>>>>
>>>> VFdata
>>>>
>>>> AffyBatch object
>>>> size of arrays=1050x1050 features (11 kb)
>>>> cdf=HuGene-1_0-st-v1 (??? affyids)
>>>> number of samples=7
>>>> Error in getCdfInfo(object) :
>>>> ?Could not obtain CDF environment, problems encountered:
>>>> Specified environment does not contain HuGene-1_0-st-v1
>>>> Library - package hugene10stv1cdf not installed
>>>> Bioconductor - hugene10stv1cdf not available
>>>> In addition: Warning message:
>>>> missing cdf environment! in show(AffyBatch)
>>>> and going on
>>>>
>>>> eset = exprs(rma(VFdata))
>>>>
>>>> Error in getCdfInfo(object) :
>>>> ?Could not obtain CDF environment, problems encountered:
>>>> Specified environment does not contain HuGene-1_0-st-v1
>>>> Library - package hugene10stv1cdf not installed
>>>> Bioconductor - hugene10stv1cdf not available
>>>> Error in exprs(rma(VFdata)) :
>>>> ?error in evaluating the argument 'object' in selecting a method for
>>>> function 'exprs'
>>>>
>>>>
>>>>
>>>> I'm very inexperienced in terms of stuff like that. A answer for
>>>> dummies would be much appreciated.
>>>> Thanks
>>>> Christoph
>>>>
>>>>
>>
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
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