[BioC] Mas5, normalization method, error

[Wolfgang Huber]

Dear Yisong

When I run the following code,

   library("affy")
   raw.data<-ReadAffy("E-MEXP-1478-raw-cel-1594215448.cel")
   mas5.data<-mas5(raw.data);

I get

background correction: mas
PM/MM correction : mas
expression values: mas
background correcting...Errore in getCdfInfo(object) :
   Could not obtain CDF environment, problems encountered:
Specified environment does not contain CINT06a520380F
Library - package cint06a520380fcdf not installed
Bioconductor - cint06a520380fcdf not available

Can you also provide the CDF package for your array? It might be worth 
getting in touch with the person who designed the array to make sure 
MAS5 is appropriate for it (e.g. does it have probesets, and mismatch 
probes?)

PS Luckily, the EBIs http servers have no problem and your cel file used 
in the above example is here:
http://www.ebi.ac.uk/~huber/stuff/E-MEXP-1478-raw-cel-1594215448.cel


 > sessionInfo()
R version 2.9.0 Under development (unstable) (2008-11-27 r47025)
x86_64-unknown-linux-gnu

locale:
LC_CTYPE=it_IT.UTF-8;LC_NUMERIC=C;LC_TIME=it_IT.UTF-8;LC_COLLATE=it_IT.UTF-8;LC_MONETARY=C;LC_MESSAGES=it_IT.UTF-8;LC_PAPER=it_IT.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=it_IT.UTF-8;LC_IDENTIFICATION=C

attached base packages:
[1] tools     stats     graphics  grDevices datasets  utils     methods
[8] base

other attached packages:
[1] affy_1.21.0    Biobase_2.3.3  fortunes_1.3-5

loaded via a namespace (and not attached):
[1] affyio_1.11.2        preprocessCore_1.5.2


Best wishes
      Wolfgang

----------------------------------------------------
Wolfgang Huber, EMBL-EBI, http://www.ebi.ac.uk/huber

Yisong Zhen ha scritto:
> Dear Wolfgang,
> 
> The attachment is our array data (CEL format). Our ftp server has some
> problem so I have to send them by email and not cc it to bioconductor
> mail list. These arrays are customed chips. I am not familiar with the
> MAS5 algorithm. I think something is missed in these chips. I hope you
> can clarify it so that I can proceed to my next step to get quality
> parameters.
> 
> I am looking forward to your reply. Thanks again for your help.
> 
> Yisong
> 
> On Fri, Nov 14, 2008 at 4:19 PM, Wolfgang Huber <huber at ebi.ac.uk> wrote:
>> Dear Yisong
>>
>> I am not promising that this will fix the problem, but can you please try
>> this, and report the error, with the latest release version of R and
>> Bioconductor rather than these older ones?
>>
>> Also, and probably more importantly, can you make available some raw data
>> (the CEL files or the raw.data object) with which you get this problem -  so
>> that we can debug this.
>>
>> Best wishes
>>     Wolfgang
>>
>> ----------------------------------------------------
>> Wolfgang Huber, EMBL-EBI, http://www.ebi.ac.uk/huber
>>
>>
>> Yisong Zhen ha scritto:
>>> Dear All,
>>>
>>> I try to use the mas5 to normalize my data. but it failed. However, I
>>> can use RMA method to normlize the data.
>>>
>>> The following is the error message:
>>> Loading required package: affyio
>>> Loading required package: preprocessCore
>>>> raw.data<-ReadAffy();
>>>> mas5.data<-mas5(raw.data);
>>> background correction: mas
>>> PM/MM correction : mas
>>> expression values: mas
>>> background correcting...Error in as.vector(data) : NA/NaN/Inf in
>>> foreign function call (arg 1).
>>>
>>> Here is my sessioninfo():
>>>
>>>> sessionInfo() ;
>>> R version 2.7.2 (2008-08-25)
>>> ia64-unknown-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     stats     graphics  grDevices utils     datasets  methods
>>> [8] base
>>>
>>> other attached packages:
>>> [1] cint06a520380fcdf_1.18.0 affy_1.18.2              preprocessCore_1.2.1
>>> [4] affyio_1.8.1             Biobase_2.0.1
>>>
>>> Thanks very much for any help.
>>>
>>> Yisong