Hi Joseph,

 

I tried exactly the same command as in
https://stat.ethz.ch/pipermail/bioconductor/2007-December/020468.html:

***** R Code ****
 > library(makePlatformDesign)
 > makePDpackage("AFFY_TILING.bpmap",file1="AFFY_TILING.cif", 
manufacturer="affymetrix", type="tiling")
 

I even renamed the file names of .bpmap and .cif, but I still got the same
error:

 

affymetrix tiling 

The package will be called pd.affy.tiling 

Error in makeBPMAPenv(designFile, file1, genomebuild = genomebuild) : 

  SET_VECTOR_ELT() can only be applied to a 'list', not a 'NULL'

 

How did you get this problem solved? Thanks!

 

Feng

 

  _____  

From: joseph [mailto:jdsandjd@yahoo.com] 
Sent: Thursday, January 24, 2008 8:32 PM
To: Feng Tian
Cc: bioconductor@stat.math.ethz.ch
Subject: Re: About Affy TilingArray makePDpackage

 

I refer you to Naira's response where you might find the solution:
https://stat.ethz.ch/pipermail/bioconductor/2007-December/020468.html
However, I did not go any further because I did not have enough memory on my
PC. Also, you can check Henrik's solution to the memory problem
https://stat.ethz.ch/pipermail/bioconductor/2007-December/020479.html
Good Luck

----- Original Message ----
From: Feng Tian <firmly@gmail.com>
To: jdsandjd@yahoo.com; jmacdon@med.umich.edu
Cc: Frank Liu <xliu26@uic.edu>; parantu shah <parantu.shah@gmail.com>
Sent: Thursday, January 24, 2008 2:12:41 PM
Subject: About Affy TilingArray makePDpackage

Hi, Joseph,

>From the Bioconductor mail list,  I found that you had ever met the same
problem as I do now. When trying to create environment for Drosophila tiling
array, 

> makePDpackage("Dm35b_MF_v02-3_BDGPv4h.bpmap", file1="Dm35b_MF_v02.cif",
manufacturer="affymetrix", type="tiling") 

I got the same error:

affymetrix tiling
The package will be called pd.dm35b.mr.v02.3.bdgpv4h.nr
Error in makeBPMAPenv(designFile, file1, genomebuild = genomebuild) : 
  SET_VECTOR_ELT() can only be applied to a 'list', not a 'NULL'

Have you solved your problems, and how? Thanks!



I'm using the latest version of R and packages:

> sessionInfo() 
R version 2.6.1 (2007-11-26)
powerpc-apple-darwin8.10.1

locale:
C

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

other attached packages: 
 [1] makePlatformDesign_1.2.0 oligo_1.2.2              oligoClasses_1.0.3
 [4] affxparser_1.10.2        AnnotationDbi_1.0.6      preprocessCore_1.0.0
 [7] RSQLite_0.6-4            DBI_0.2-4                Biobase_1.16.2 
[10] affyio_1.6.1

loaded via a namespace (and not attached):
[1] rcompgen_0.1-17




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