HI Henrik,
I was a little bit investigating the error and I found out that some
of the fragments reported in NetAffx files are really long.
Why they got a negative value of -32768 and not a positive one?
Robert
On Jun 1, 7:16 pm, "Ivanek, Robert" <robert.iva...@fmi.ch> wrote:
> Hi Henrik,
>
> Thanks for the answer and also the ACS file.
> I have one more question regarding the UFL file generation.
>
> I tried it by using the NettAffx and I got the following error:
>
> R> ufl <- AromaUflFile$allocateFromCdf(cdf, nbrOfEnzymes=2,
> tags=c("na30", "RI20100601"))
> R> csv <- AffymetrixNetAffxCsvFile$byChipType(chipType, tags=".na30");
> R> units <- importFrom(ufl, csv);
> Warning messages:
> 1: In updateDataColumn.AromaTabularBinaryFile(this, .con = con, .hdr =
> hdr, :
> Values to be assigned were out of range [-32767,32768] and therefore
> censored to fit the range.
> 2: In updateDataColumn.AromaTabularBinaryFile(this, .con = con, .hdr =
> hdr, :
> Values to be assigned were out of range [-32767,32768] and therefore
> censored to fit the range.
>
> R> csv <- AffymetrixNetAffxCsvFile$byChipType(chipType,
> tags=".cn.na30");
> R> units <- importFrom(ufl, csv);
> Warning messages:
> 1: In updateDataColumn.AromaTabularBinaryFile(this, .con = con, .hdr =
> hdr, :
> Values to be assigned were out of range [-32767,32768] and therefore
> censored to fit the range.
> 2: In updateDataColumn.AromaTabularBinaryFile(this, .con = con, .hdr =
> hdr, :
> Values to be assigned were out of range [-32767,32768] and therefore
> censored to fit the range.
>
> And the summary produce the following
> R> summary(ufl)
> length length.02
> Min. :-32768 Min. :-32768
> 1st Qu.: 614 1st Qu.: 541
> Median : 1146 Median : 997
> Mean : 1601 Mean : 1466
> 3rd Qu.: 2195 3rd Qu.: 2000
> Max. : 22095 Max. : 30002
> NA's :230775 NA's :230775
>
> Would you be so kind and build also the UFL and UGP files?
>
> Best Regards
>
> Robert
>
> On May 30, 7:27 pm, Henrik Bengtsson <h...@stat.berkeley.edu> wrote:
>
> > 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
> > > "aroma.affymetrix" group with websitehttp://www.aroma-project.org/.
> > > To post to this group, send email to aroma-affymetrix@googlegroups.com
> > > To unsubscribe and other options, go tohttp://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.
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