Hi.

On Wed, May 26, 2010 at 3:24 PM, Ivanek, Robert <robert.iva...@fmi.ch> wrote:
> Dear Sir or Madam,
>
> I would like to analyse the copy number variation data from Affymetrix
> Mouse Diversity Array. I have not found any information on your website
> about this particular array.

I have created page for this:

http://aroma-project.org/chipTypes/MOUSEDIVm520650

> I have tried to build the annotation files
> which are required by aroma but without success. I have few questions
> regarding that:
>
> 1: Is aroma.affymetrix able to analyse the "Mouse Diversity Array" ?

Yes, because there should be no reason why it shouldn't - it uses a
standard CDF etc.  As you've noted, UGP (and UFL) files have not been
created by anyone yet.

For CN analysis, at least the UGP (genome positions) annotation data
file needs to be there.

>
> 2: I tried to build the "UGP" file directly from NetAffx annotation
> files using the code on your website, however I am getting the following
> error.
>
> ##
> library("aroma.affymetrix")
> ##
> ## create UGP from NetAffx files
> cdf <- AffymetrixCdfFile$byChipType("MOUSEDIVm520650")
> ##
> ## Creates an empty UGP file for the CDF, if missing.
> ugp <- AromaUgpFile$allocateFromCdf(cdf, tags=c("na30", "RI20100526"))
> ##
> ## Import NetAffx unit position data
> csv <- AffymetrixNetAffxCsvFile$byChipType("MOUSEDIVm520650",
> otags=".na30")
>
> Error in list(`AffymetrixNetAffxCsvFile$byChipType("MOUSEDIVm520650",
> tags = ".na30")` = <environment>,  :
>
> [2010-05-26 15:11:00] Exception: File format error of the tabular file
> ('annotationData/chipTypes/MOUSEDIVm520650/NetAffx/MOUSEDIVm520650.na30.annot.csv'):
>  \
> line 1 did not have 12 elements
>  at throw(Exception(...))
>  at throw.default("File format error of the tabular file ('",
> getPathname(this), "'): ", ex$message)
>  at throw("File format error of the tabular file ('",
> getPathname(this), "'): ", ex$message)
>  at value[[3]](cond)
>  at tryCatchOne(expr, names, parentenv, handlers[[1]])
>  at tryCatchList(expr, classes, parentenv, handlers)
>  at tryCatch({
>  at verify.TabularTextFile(this, ...)
>  at verify(this, ...)
>  at this(...)
>  at newInstance.Class(clazz, ...)
>  at newInstance(clazz, ...)
>  at newInstance.Object(static, pathname)
>  at newInstance(static, pathname)
>  at method(static, ...)
>  at AffymetrixNetAffxCsvFile$byChipType("MOUSEDIVm520650", tags =
> ".na30")
> In addition: Warning message:
> In read.table(3L, header = TRUE, colClasses = c(NA_character_,
> NA_character_,  :
>  not all columns named in 'colClasses' exist

I had a look at the MOUSEDIVm520650.na30.annot.csv file.  The line
containing column names, that is:

"Probe Set ID","dbSNP RS ID","Chromosome","Physical
Position","Strand","Cytoband","Allele A","Allele B","Associated
Gene","Genetic Map","Fragment Enzyme Type Length Start Stop",

contains a trailing comma (,) that shouldn't be there ("file format
error").  This cause R to think there should be 12 and not 11 columns
in the data set.  Open the file in an editor and remove that trailing
comma and any whitespace after "Fragment Enzyme Type Length Start
Stop".  Then save the file.  That should solve the problem.

The other CSV file - MOUSEDIVm520650.cn.na30.annot.csv - does not have
this problem.

>
>
> 3. I tried it also by using the "manual" approach using the
> tab=delimited file, however it seems to me that the mitochondria probes
> are skipped  (NA values in ugp[,1] but valid values in ugp[,2]).

The Affymetrix NetAffx CSV files use s "M" for the mitochondria
chromosome.  In aroma we encode this by integer 25.

> Another
> problem is that some positions for other chromosomes are not loaded in
> properly (valid values in ugp[,1] but NA values in ugp[,2]).

You don't show how you read the data "manually", so it is hard to say
what you are doing wrong here.  But note that there are quite a few
arguments in read.table() that you need to set correctly in order to
read Affymetrix NetAffx CSV files (it doesn't make easier that
Affymetrix changes the file format once in a while and have stray
erroneous symbols such as the above comma).

Also, search our forum for 'MOUSEDIVm520650', because about a year ago
David Rosenberg disscussed this chip type and I think he did create
various annotation data files for the chip type.  This was before the
chip type was publicly announced by Affymetrix.

/Henrik

>
>
> Here is the sessionInfo:
>
> R version 2.11.0 (2010-04-22)
> x86_64-unknown-linux-gnu
>
> locale:
>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
> LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8     LC_MONETARY=C
>  [6] LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8       LC_NAME=C
> 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] aroma.affymetrix_1.6.0 aroma.apd_0.1.7        affxparser_1.20.0
> R.huge_0.2.0           aroma.core_1.6.0       aroma.light_1.16.0
>  [7] matrixStats_0.2.1      R.rsp_0.3.6            R.cache_0.3.0
> R.filesets_0.8.1       digest_0.4.2           R.utils_1.4.0
> [13] R.oo_1.7.2             R.methodsS3_1.2.0      RColorBrewer_1.0-2
>
> loaded via a namespace (and not attached):
> [1] tools_2.11.0
>
>
>
> Best Regards
>
> Robert
>
>
>
>
>
> --
> Robert Ivanek
> Postdoctoral Fellow Schuebeler Group
> Friedrich Miescher Institute
> Maulbeerstrasse 66
> 4058 Basel / Switzerland
> Office phone: +41 61 697 6100
>
> --
> 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 
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>

-- 
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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