[BioC] affylmGUI segfault on "pd.ragene.1.0.st.v1"

[James W. MacDonald]

Hi Harry,

Wolfgang Huber wrote:
> 
> Hi Harry & Matt
> 
> re your second question, about the CDF package: the way the affy package 
> works, it expects a package with name "ragene10stv1cdf", containing an 
> R-environment of that same name, with the probeset definitions for that 
> chip.
> 
> Note that the CDF packages that the "affy" package uses are *not* the 
> same as the platform design packages that the "oligo" package uses.
> Essentially: affy = old, tried and tested, but only works for convential 
> Affymetrix genechips for mRNA analysis with genechip using 3' probe sets.
> oligo = newer, more general, also suitable for more recent chip types 
> inclduding for genotyping..
> 
> It seems that you want affy and CDF packages. The make.cdf.package 
> function from the makecdfenv package is what you or Matt would want to 
> use to build these.
> 
> Jim McDonald (cc-ed) has written an overview over the software tools for 
> analysing Affymetrix arrays, unfortunately I could not figure out how to 
> find it from the Bioconductor webpage, so maybe he can help with that.

I don't know if/where the overview lives. It may not have made it onto 
the website as yet - perhaps Herve knows?

> 
> 
> Best wishes
>  Wolfgang
> 
> Harry Mangalam ha scritto:
>> Hi All,
>>
>> I've been trying to get affylmGUI to run on my laptop (3GB, Ubuntu 
>> 8.04, R as below:
>> =====
>>> sessionInfo()
>> R version 2.8.0 (2008-10-20)
>> i686-pc-linux-gnu
>>
>> locale:
>> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C 
>>
>>
>> attached base packages:
>> [1] tools     tcltk     stats     graphics  grDevices utils     datasets
>> [8] methods   base
>>
>> other attached packages:
>> [1] affylmGUI_1.16.0     affy_1.16.0          preprocessCore_1.0.0
>> [4] affyio_1.6.1         Biobase_2.2.1        limma_2.16.3

This sessionInfo is different than what you should get if you run the 
commands below. For instance, oligo isn't loaded. Additionally, you 
don't really want to load both oligo and affy, as they share some 
function names so you will end up with masking of things you will need, 
such as rma(). In other words, if you load oligo and then affylmGUI, the 
rma() that you will get comes from affy rather than oligo.

So you are going to be unable to use affylmGUI to analyze these data, as 
this package assumes you are planning to use affy to do the 
normalization/summarization, and as you know this is done with oligo for 
these chips. So at this time your only recourse is to use the 
command-line tools in the oligo package.

The segfault is irrelevant to this analysis, but hopefully Keith 
Satterley will see this thread (or you could contact him directly) in 
case you want to use affylmGUI for other analyses.

Best,

Jim


>> =====
>> The commands to start affylmGUI are:
>> library("pd.ragene.1.0.st.v1") # the array set, from Matt Settles
>> library("oligo")
>> library("affylmGUI")
>> affylmGUI()
>>
>> when I try to load data, whether my own (or the estrogen data set), it 
>> segfaults at the same place:
>> After I select a working directory, and select the targets file 
>> (included below), [R churns for a few seconds], and give the new data 
>> set a name, I can see that the data is 'available' via the data tree 
>> in the left panel.
>>
>> At the point where I try to view the RNA targets via Menu -> RNA 
>> Targets -> RNA Targets, and release the mouse button, it segfaults, 
>> leaving the traceback:
>>
>> http://moo.nac.uci.edu/~hjm/affylmGUI.traceback
>>
>> As I said above, this is the case if it's my data or the estrogen data 
>> set.
>>
>> If I try to bypass that step and go direct to normalization (with my 
>> data), it will eventually emit the error that I don't have the correct 
>> CDF environment:
>>
>> ==== Error message ====
>> Error in getCdfInfo(object): Could not obtain CDF environment, 
>> problems encountered: Specified environment does not contain 
>> RaGene-1_0-st-v1 Library - package ragene10stv1cdf not installed. Data 
>> for package affy did not contain ragene10stv1cdf Bioconductor - 
>> ragene10stv1cdf not available
>> =======================
>>
>> This despite loading without error the correct (from Matt Settles) 
>> library beforehand. > library("pd.ragene.1.0.st.v1")
>> Does the spelling variant muck it up? 
>> Best wishes,
>> harry
>>
>>
>> ==== targets.txt (whitespaces are TABS) ====
>>
>> Name    FileName        Target
>> AB.1    0908F-02_AB_1.CEL       AB_Only
>> AB.2    0908F-02_AB_2.CEL       AB_Only
>> AB.3    0908F-02_AB_3.CEL       AB_Only
>> CIQ.1   0908F-02_CIQ_1.CEL      CIQ_Only
>> CIQ.2   0908F-02_CIQ_2.CEL      CIQ_Only
>> CIQ.3   0908F-02_CIQ_3.CEL      CIQ_Only
>> CIQ+AB.1        0908F-02_CIQ_AB_1.CEL   CIQ_AB_CoTreatment
>> CIQ+AB.2        0908F-02_CIQ_AB_2.CEL   CIQ_AB_CoTreatment
>> CIQ+AB.3        0908F-02_CIQ_AB_3.CEL   CIQ_AB_CoTreatment
>> Untreated.1     0908F-02_Untreated_1.CEL        CONTROL
>> Untreated.2     0908F-02_Untreated_2.CEL        CONTROL
>> Untreated.3     0908F-02_Untreated_3.CEL        CONTROL
>>
> 

-- 
James W. MacDonald, M.S.
Biostatistician
Hildebrandt Lab
8220D MSRB III
1150 W. Medical Center Drive
Ann Arbor MI 48109-0646
734-936-8662