Hi,
I followed the advice to filter out some PCR fragment based on length
( < 450 | > 2000).
But i still run into the same error (see below). I am not sure what
went wrong.......
Thanks,
Yupu
20110119 00:18:09| Array #1 of 36 ('KP_17124_NT_MOUSEDIVm520650')...
V1 V2
Min. : 450 Min. : 450
1st Qu.: 700 1st Qu.: 689
Median : 958 Median : 945
Mean : 1065 Mean : 1050
3rd Qu.: 1408 3rd Qu.: 1385
Max. : 2000 Max. : 2000
NA's :1225618 NA's :1224870
int [1:2291870] 1 2 3 4 5 6 7 8 9 10 ...
UflSnpInformation:
Name: MOUSEDIVm520650
Tags: na30,mm9,filter450-2000,HB20101105
Full name: MOUSEDIVm520650,na30,mm9,filter450-2000,HB20101105
Pathname: annotationData/chipTypes/MOUSEDIVm520650/
MOUSEDIVm520650,na30,mm9,filter450-2000,HB20101105.ufl
File size: 9.38 MB (9835569 bytes)
RAM: 18.76 MB
Chip type: MOUSEDIVm520650
Number of enzymes: 2
20110119 00:18:17| Setting up predefined target functions...
20110119 00:18:17| Target type: zero
20110119 00:18:17| Setting up predefined target functions...done
20110119 00:18:17| Getting cell matrix map...
'UnitGroupCellMatrixMap' int [1:2458673, 1] 25 26 27 28 29 30 31
32 33 34 ...
20110119 00:18:20| Getting cell matrix map...done
20110119 00:18:20| Getting theta estimates...
20110119 00:18:21| Thetas:
num [1:2458673, 1] 0 0 0 0 0 0 0 0 0 0 ...
num [1:2458673, 1] 0 0 0 0 0 0 0 0 0 0 ...
V1
Min. :0
1st Qu.:0
Median :0
Mean :0
3rd Qu.:0
Max. :0
20110119 00:18:21| Getting theta estimates...done
20110119 00:18:21| Calculating total signals...
20110119 00:18:22| Total thetas:
num [1:2458673] 0 0 0 0 0 0 0 0 0 0 ...
20110119 00:18:22| Calculating total signals...done
20110119 00:18:22| Normalizing log2 signals...
20110119 00:18:22| Log2 signals:
num [1:2458673] -Inf -Inf -Inf -Inf -Inf ...
Error in list(`source("yupu.preprocess.Mm.R")` = <environment>,
`eval.with.vis(ei, envir)` = <environment>, :
[2011-01-19 00:18:23] Exception: Cannot fit normalization function to
enzyme, because there are no (finite) data points that are unique to
this enzyme: 1
at throw(Exception(...))
On Jan 14, 8:39 am, Henrik Bengtsson <henrik.bengts...@aroma-
project.org> wrote:
> Hi,
>
> have a look at thread 'MOUSEDIVm520650 and CRMAv2' started on Nov 5, 2010:
>
> https://groups.google.com/d/topic/aroma-affymetrix/MEGCiXrPA80/discus...
>
> There we noted that this is because Affymetrix no longer filters the
> fragment lengths in its annotation files. This means that all SNPs
> have fragment lengths reported for both enzymes in our UFL annotation
> files. In order to fit the fragment-length model, there have to be
> SNPs for which only one of the two enzymes have a fragment length.
>
> The workaround found, as explained in that thread, is to create a UFL
> where one turn very short or very long fragment length values intoNAs.
> In my Nov 5 reply to the above threat, there is a code example
> showing how to drop lengths < 450 bp or > 2000 bp creating a new UFL
> file.
>
> Hans-Ulrich (bcc:ed), did you create such a UFL file? Did that solve
> the problem? Would you mind sharing that UFL file here - I can upload
> it tohttp://aroma-project.org/chipTypes/MOUSEDIVm520650/. That will
> save others from having to do the same.
>
> BTW, it would be more convenient to add filter options to
> FragmentLengthNormalization. For a discussion on implementing that,
> see thread 'GenomeWideSNP_6 hg19' started on Dec 10, 2010:
>
> https://groups.google.com/d/topic/aroma-affymetrix/FgETqjjYz1U/discus...
>
> /Henrik
>
>
>
> On Thu, Jan 13, 2011 at 10:50 PM, yupu <yupuli...@gmail.com> wrote:
> > Hi, I have been using aroma to analysis our SNP6.0 array for a while.
> > Now we got data on the Mouse diversity array (MouseDIV__m520650).
>
> > I ran into problem at the fragmentation length normalization step --
> > same
> > ashttp://www.mail-archive.com/aroma-affymetrix@googlegroups.com/msg0145...
>
> > Error in list(`process(fln, verbose = verbose)` = <environment>,
> > `process.FragmentLengthNormalization(fln, verbose = verbose)` =
> > <environment>, :
>
> > [2011-01-13 14:31:10] Exception: Cannot fit normalization function to
> > enzyme, because there are no (finite) data points that are unique to
> > this enzyme: 1
> > at throw(Exception(...))
> > at throw.default("Cannot fit normalization function to enzyme,
> > because there a
> > at throw("Cannot fit normalization function to enzyme, because there
> > are no (f
> > at normalizeFragmentLength.default(y, fragmentLengths = fl,
> > targetFcns = targe
> > at normalizeFragmentLength(y, fragmentLengths = fl, targetFcns =
> > targetFcns, s
> > at process.FragmentLengthNormalization(fln, verbose = verbose)
> > at process(fln, verbose = verbose)
> > 20110113 14:31:10| Normalizing log2 signals...done
> > 20110113 14:31:10| Array #1 of 36
> > ('KP_17124_NT_MOUSEDIVm520650')...done
> > 20110113 14:31:10|Normalizing set for PCR fragment-length
> > effects...done
>
> > I am just wondering if there is any update on this issue.
>
> > Thanks,
> > Yupu
>
> > --
> > 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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--
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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