[aroma.affymetrix] bug in function pdInfo2Cdf

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[aroma.affymetrix] bug in function pdInfo2Cdf

Hooiveld, Guido
Dear Henrik,
 
I would like to report a problem with the function pdInfo2Cdf.R
I know this function is not part of the core functionality of aroma.affymetrix, but i thought it still would be good to inform you about the error i found.
Meanwhile I found out it is caused by line 71:
the argument 'pdName' should actually be 'pdpkg' in
line 71 - filename <- sprintf("%s.cdf", pdName);
 
If I apply the above-mentioned modification, source the modified function 'pdInfo2Cdf_MOD.R, and then run the function everything goes fine (see below).
 
For your convenience I have uploaded a CEL file required to execute the function (for testing purposes):
Note: link is alive for 5 days, and/or allows max 20 downloads.
 
Regards,
Guido
 
 
> library(aroma.affymetrix)
<<SNIP>>
> pdInfo2Cdf("pd.mogene.1.1.st.v1", "MouseBrain_1.CEL");
<<SNIP>>
PdInfo2Cdf()...
Error in sprintf("%s.cdf", pdName) : object 'pdName' not found
In addition: Warning message:
In fcn(...) : Packages reordered in search path: package:oligo
 
> source("pdInfo2Cdf_MOD.R")
> pdInfo2Cdf("pd.mogene.1.1.st.v1", "MouseBrain_1.CEL");
PdInfo2Cdf()...
Loading required package: pd.mogene.1.1.st.v1
 Reading auxillary CEL file...
Platform design info loaded.
Reading in : MouseBrain_1.CEL
 Reading auxillary CEL file...done
 Querying Platform Design database...
 Querying Platform Design database...done
 Creating list from query table...
 Creating list from query table...done
 Creating CDF list structure...
  Creating CDF list for 241576 units
 Creating CDF list structure...done
 Writing CDF file...
Writing CDF file...
  Pathname: pd.mogene.1.1.st.v1.cdf
  Writes CDF header and unit names...
  Writes CDF header and unit names...done
  Writes QC units...
  Writes QC units...done
  Writes 241576 units...
  Writes 241576 units...done
Writing CDF file...done
 Writing CDF file...done
PdInfo2Cdf()...done
>
> sessionInfo()
R version 2.12.0 (2010-10-15)
Platform: x86_64-unknown-linux-gnu (64-bit)
 
locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C             
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8   
 [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8  
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                
 [9] LC_ADDRESS=C               LC_TELEPHONE=C           
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C      
 
attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base    
 
other attached packages:
 [1] pdInfoBuilder_1.14.1   oligoClasses_1.12.1    RSQLite_0.9-4        
 [4] DBI_0.2-5              Biobase_2.10.0         aroma.affymetrix_1.8.0
 [7] aroma.apd_0.1.7        affxparser_1.22.0      R.huge_0.2.0         
[10] aroma.core_1.8.0       aroma.light_1.18.2     matrixStats_0.2.2    
[13] R.rsp_0.4.0            R.cache_0.3.0          R.filesets_0.9.1     
[16] digest_0.4.2           R.utils_1.5.8          R.oo_1.7.4           
[19] oligo_1.14.0           R.methodsS3_1.2.1    
 
loaded via a namespace (and not attached):
[1] affyio_1.19.2         Biostrings_2.18.0     IRanges_1.8.3       
[4] preprocessCore_1.12.0 splines_2.12.0      
------------------------------------------------
Guido Hooiveld, PhD
Nutrition, Metabolism & Genomics Group
Division of Human Nutrition
Wageningen University
Biotechnion, Bomenweg 2
NL-6703 HD Wageningen
the Netherlands
tel: (+)31 317 485788
fax: (+)31 317 483342
internet:   http://nutrigene.4t.com
email:      [hidden email]
 

--
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.
 
 
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Re: [aroma.affymetrix] bug in function pdInfo2Cdf

Henrik Bengtsson-4
Hi Guido,

thanks a bunch for this.

I've made a patch available until next release of aroma.affymetrix.
Just do the following (only once) to install the patches:

source("http://aroma-project.org/hbLite.R");
hbInstall("aroma.affymetrix");

FYI, I did use the 'pdName' variable (which is defined later in the
code) and not the 'pdpkg', because that is what the original author(s)
used to generate the CDF filename.

/Henrik

On Fri, Dec 3, 2010 at 1:07 PM, Hooiveld, Guido <[hidden email]> wrote:

> Dear Henrik,
>
> I would like to report a problem with the function pdInfo2Cdf.R
> I know this function is not part of the core functionality of
> aroma.affymetrix, but i thought it still would be good to inform you about
> the error i found.
> Meanwhile I found out it is caused by line 71:
> the argument 'pdName' should actually be 'pdpkg' in
> line 71 - filename <- sprintf("%s.cdf", pdName);
>
> If I apply the above-mentioned modification, source the modified function
> 'pdInfo2Cdf_MOD.R, and then run the function everything goes fine (see
> below).
>
> For your convenience I have uploaded a CEL file required to execute the
> function (for testing purposes):
> https://sendit.wur.nl/Download.aspx?id=e0c9eea2-5f72-454c-873d-f1a215f57d1c
> Note: link is alive for 5 days, and/or allows max 20 downloads.
>
> Regards,
> Guido
>
>
>> library(aroma.affymetrix)
> <<SNIP>>
>> pdInfo2Cdf("pd.mogene.1.1.st.v1", "MouseBrain_1.CEL");
> <<SNIP>>
> PdInfo2Cdf()...
> Error in sprintf("%s.cdf", pdName) : object 'pdName' not found
> In addition: Warning message:
> In fcn(...) : Packages reordered in search path: package:oligo
>
>> source("pdInfo2Cdf_MOD.R")
>> pdInfo2Cdf("pd.mogene.1.1.st.v1", "MouseBrain_1.CEL");
> PdInfo2Cdf()...
> Loading required package: pd.mogene.1.1.st.v1
>  Reading auxillary CEL file...
> Platform design info loaded.
> Reading in : MouseBrain_1.CEL
>  Reading auxillary CEL file...done
>  Querying Platform Design database...
>  Querying Platform Design database...done
>  Creating list from query table...
>  Creating list from query table...done
>  Creating CDF list structure...
>   Creating CDF list for 241576 units
>  Creating CDF list structure...done
>  Writing CDF file...
> Writing CDF file...
>   Pathname: pd.mogene.1.1.st.v1.cdf
>   Writes CDF header and unit names...
>   Writes CDF header and unit names...done
>   Writes QC units...
>   Writes QC units...done
>   Writes 241576 units...
>   Writes 241576 units...done
> Writing CDF file...done
>  Writing CDF file...done
> PdInfo2Cdf()...done
>>
>> sessionInfo()
> R version 2.12.0 (2010-10-15)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>  [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
>  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
>  [1] pdInfoBuilder_1.14.1   oligoClasses_1.12.1    RSQLite_0.9-4
>  [4] DBI_0.2-5              Biobase_2.10.0         aroma.affymetrix_1.8.0
>  [7] aroma.apd_0.1.7        affxparser_1.22.0      R.huge_0.2.0
> [10] aroma.core_1.8.0       aroma.light_1.18.2     matrixStats_0.2.2
> [13] R.rsp_0.4.0            R.cache_0.3.0          R.filesets_0.9.1
> [16] digest_0.4.2           R.utils_1.5.8          R.oo_1.7.4
> [19] oligo_1.14.0           R.methodsS3_1.2.1
>
> loaded via a namespace (and not attached):
> [1] affyio_1.19.2         Biostrings_2.18.0     IRanges_1.8.3
> [4] preprocessCore_1.12.0 splines_2.12.0
> ------------------------------------------------
> Guido Hooiveld, PhD
> Nutrition, Metabolism & Genomics Group
> Division of Human Nutrition
> Wageningen University
> Biotechnion, Bomenweg 2
> NL-6703 HD Wageningen
> the Netherlands
> tel: (+)31 317 485788
> fax: (+)31 317 483342
> internet:   http://nutrigene.4t.com
> email:      [hidden email]
>
>
> --
> 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 with website http://www.aroma-project.org/.
> To post to this group, send email to [hidden email]
> To unsubscribe and other options, go to http://www.aroma-project.org/forum/
>

--
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 with website http://www.aroma-project.org/.
To post to this group, send email to [hidden email]
To unsubscribe and other options, go to http://www.aroma-project.org/forum/