Hi,
see below.
On Wed, Jan 19, 2011 at 6:34 PM, yupu <yupuli...@gmail.com> wrote:
> 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
These are all zeros. You have most likely forgotten to run fit() on
the probe-level modelling step (AvgCnPlm).
> 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 ...
This says that too.
/Henrik
> 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.
>>
>> > 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.
>
>
> 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.
You received this message because you are subscribed to the Google Groups
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