Hi,
if you google "Cannot fit normalization function to enzyme, because
there are no (finite) data points that are unique to this enzyme"
you'll find that this problem have been reported at least twice
before;
you have most likely forgotten to do fit(plm).
/Henrik
On Wed, Aug 26, 2009 at 10:15 PM, Max Moldovan<max.moldo...@gmail.com> wrote:
>
> Hi Henrik,
>
> Yes, you are right and the previous exception was due to annotation
> files misspecification (.acs was dislocated).
>
> I move through the “CRMA v2 method” vignette you recommended and got
> one more exception at cesN <- process(fln, verbose=verbose):
>
> #######################
> [2009-08-27 14:30:09] 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)
> Normalizing log2 signals...done
> Array #1 of 66 ('APOC121')...done
> Normalizing set for PCR fragment-length effects...done
> #######################
>
> First I thought it could be due to NaNs produced at csN <- process
> (bpn, verbose=verbose), but I appropriately shifted the numbers by plm
> <- AvgCnPlm(csN, mergeStrands=TRUE, combineAlleles=TRUE, shift=+300),
> and still have the same exception.
>
> How do you deal with this?
>
> Thanks,
>
> Max
>
>
> On Aug 26, 6:28 pm, Henrik Bengtsson <h...@stat.berkeley.edu> wrote:
>> Hi.
>>
>> You need to download (and unzip) all necessary annotation data files
>> for the GenomeWideSNP_5 chit type:
>>
>> http://groups.google.com/group/aroma-affymetrix/web/genomewidesnp-5
>>
>> This particular problem is because it cannot find
>> GenomeWideSNP_5,HB20080710.acs.
>>
>> Instead of the code snippet, follow the vignette 'Estimation of total
>> copy numbers using the CRMA v2 method':
>>
>> http://groups.google.com/group/aroma-affymetrix/web/estimation-of-tot...
>>
>> which helps you make sure you got everything setup before starting.
>>
>> Cheers,
>>
>> HenrikOn Tue, Aug 25, 2009 at 10:43 PM, Max Moldovan<max.moldo...@gmail.com>
>> wrote:
>>
>> > Hi People,
>>
>> > I am getting started with aroma.affymetrix analysing 66 subjects
>> > genotyped on GenomeWideSNP_5 chip.
>>
>> > I have the following sequence (adopted from
>> >http://groups.google.com/group/aroma-affymetrix/web/code-snippets):
>>
>> > #######################################
>> > log <- Arguments$getVerbose(-8, timestamp=TRUE)
>> > chipType <- "GenomeWideSNP_5";
>> > cdfTags <- "Full,r2";
>> > cdf <- AffymetrixCdfFile$byChipType(chipType, tags=cdfTags)
>> > csR <- AffymetrixCelSet$byName("sleData", cdf=cdf)
>> > acc <- AllelicCrosstalkCalibration(csR, model="CRMAv2")
>> > acc <- AllelicCrosstalkCalibration(csR)
>> > csC <- process(acc, verbose=log)
>> > bpn <- BasePositionNormalization(csC, target="zero")
>> > csN <- process(bpn, verbose=log)
>> > plm <- AvgCnPlm(csN, mergeStrands=TRUE, combineAlleles=TRUE)
>> > if (length(findUnitsTodo(plm)) > 0) {
>> > fitCnProbes(plm, verbose=log)
>> > fit(plm, verbose=log)
>> > }
>> > ces <- getChipEffectSet(plm)
>> > fln <- FragmentLengthNormalization(ces, target="zero")
>> > cesN <- process(fln, verbose=log)
>> > #######################################
>>
>> > Everything appears to be fine up to bpn <-
>> > BasePositionNormalization(csC, target="zero"). However, when I get to
>> > csN <- process(bpn, verbose=log), I am getting the following screen
>> > output with the error inside, plus the program stops without further
>> > explanations (sorry for the large output, I don’t know what can help
>> > to catch the error):
>>
>> > #######################################
>> > 20090826 15:15:29|Normalization data set for probe-sequence effects...
>> > 20090826 15:15:29| Getting algorithm parameters...
>> > 20090826 15:15:29| Expanding unit indices...
>> > 20090826 15:15:29| Identifying subset of units...
>> > 20090826 15:15:29| Argument 'units':
>> > chr "-XY"
>> > 20090826 15:15:29| Argument 'unitTypes':
>> > 20090826 15:15:29| Getting GenomeInformation file...
>> > 20090826 15:15:30| Getting GenomeInformation file...done
>> > 20090826 15:15:30| Identifying units to include and exclude...
>> > 20090826 15:15:30| Argument 'units':
>> > 20090826 15:15:30| -XY
>> > 20090826 15:15:30| Selecting units by genomic location...
>> > 20090826 15:15:30| Chromosomes to exclude:
>> > Named num [1:2] 23 24
>> > - attr(*, "names")= chr [1:2] "X" "Y"
>> > 20090826 15:15:31| Selecting units by genomic location...done
>> > 20090826 15:15:31| Units to include:
>> > int [1:920928] 1 2 3 4 5 6 7 8 9 10 ...
>> > 20090826 15:15:31| Units to exclude:
>> > int [1:27319] 3666 3667 3669 3671 3674 3677 3678 3679 3680 3681 ...
>> > 20090826 15:15:31| Units:
>> > int [1:893609] 1 2 3 4 5 6 7 8 9 10 ...
>> > 20090826 15:15:31| Identifying units to include and exclude...done
>> > 20090826 15:15:31| Identifying subset of units...done
>> > 20090826 15:15:31| Identifying subset of units...
>> > 20090826 15:15:31| Argument 'units':
>> > NULL
>> > 20090826 15:15:31| Argument 'unitTypes':
>> > 20090826 15:15:31| Identifying units to include and exclude...
>> > 20090826 15:15:31| Argument 'units':
>> > NULL
>> > 20090826 15:15:31| Units to include:
>> > int [1:920928] 1 2 3 4 5 6 7 8 9 10 ...
>> > 20090826 15:15:31| Units to exclude:
>> > NULL
>> > 20090826 15:15:31| Units:
>> > int [1:920928] 1 2 3 4 5 6 7 8 9 10 ...
>> > 20090826 15:15:31| Identifying units to include and exclude...done
>> > 20090826 15:15:31| Identifying subset of units...done
>> > 20090826 15:15:31| Expanding unit indices...done
>> > 20090826 15:15:31| Expanding cell indices...
>> > 20090826 15:15:31| Identifying subset of units...
>> > 20090826 15:15:31| Argument 'units':
>> > chr "-XY"
>> > 20090826 15:15:31| Argument 'unitTypes':
>> > 20090826 15:15:31| Getting GenomeInformation file...
>> > 20090826 15:15:31| Getting GenomeInformation file...done
>> > 20090826 15:15:31| Identifying units to include and exclude...
>> > 20090826 15:15:31| Argument 'units':
>> > 20090826 15:15:31| -XY
>> > 20090826 15:15:31| Selecting units by genomic location...
>> > 20090826 15:15:31| Chromosomes to exclude:
>> > Named num [1:2] 23 24
>> > - attr(*, "names")= chr [1:2] "X" "Y"
>> > 20090826 15:15:31| Selecting units by genomic location...done
>> > 20090826 15:15:31| Units to include:
>> > int [1:920928] 1 2 3 4 5 6 7 8 9 10 ...
>> > 20090826 15:15:31| Units to exclude:
>> > int [1:27319] 3666 3667 3669 3671 3674 3677 3678 3679 3680 3681 ...
>> > 20090826 15:15:31| Units:
>> > int [1:893609] 1 2 3 4 5 6 7 8 9 10 ...
>> > 20090826 15:15:31| Identifying units to include and exclude...done
>> > 20090826 15:15:31| Identifying subset of units...done
>> > 20090826 15:15:31| Getting cell indices for subset of units...
>> > 20090826 15:15:31| Dataset class:
>> > 20090826 15:15:31| AffymetrixCelSet
>> > 20090826 15:15:31| chipType:GenomeWideSNP_5,Full,r2
>> > 20090826 15:15:31| Units:
>> > int [1:893609] 1 2 3 4 5 6 7 8 9 10 ...
>> > 20090826 15:15:32| Found cached results!
>> > 20090826 15:15:32| Getting cell indices for subset of units...done
>> > 20090826 15:15:32| Identifying subset of units...
>> > 20090826 15:15:32| Argument 'units':
>> > NULL
>> > 20090826 15:15:32| Argument 'unitTypes':
>> > 20090826 15:15:32| Identifying units to include and exclude...
>> > 20090826 15:15:32| Argument 'units':
>> > NULL
>> > 20090826 15:15:32| Units to include:
>> > int [1:920928] 1 2 3 4 5 6 7 8 9 10 ...
>> > 20090826 15:15:32| Units to exclude:
>> > NULL
>> > 20090826 15:15:32| Units:
>> > int [1:920928] 1 2 3 4 5 6 7 8 9 10 ...
>> > 20090826 15:15:32| Identifying units to include and exclude...done
>> > 20090826 15:15:32| Identifying subset of units...done
>> > 20090826 15:15:32| Getting cell indices for subset of units...
>> > 20090826 15:15:32| Dataset class:
>> > 20090826 15:15:32| AffymetrixCelSet
>> > 20090826 15:15:32| chipType:GenomeWideSNP_5,Full,r2
>> > 20090826 15:15:32| Units:
>> > int [1:920928] 1 2 3 4 5 6 7 8 9 10 ...
>> > 20090826 15:15:33| Found cached results!
>> > 20090826 15:15:33| Getting cell indices for subset of units...done
>> > 20090826 15:15:33| Expanding cell indices...done
>> > 20090826 15:15:33| Getting algorithm parameters...done
>> > 20090826 15:15:33| Normalizing 66 arrays...
>> > 20090826 15:15:33| Path:
>> > probeData/sleData,ACC,ra,-XY,BPN,-XY/GenomeWideSNP_5...
>> > 20090826 15:15:33| Array #1 ('APOC121') of 66...
>> > 20090826 15:15:33| Compressing model parameter to a short format...
>> > 20090826 15:15:33| Compressing model parameter to a short format...done
>> > 20090826 15:15:33| Fitting model for current array...
>> > 20090826 15:15:33| Fitting normalization function for one array...
>> > 20090826 15:15:33| Full name: APOC121
>> > 20090826 15:15:33| Getting algorithm parameters...
>> > 20090826 15:15:33| Passed internally
>> > 20090826 15:15:33| Cells:
>> > int [1:4377272] 2362002 2359836 2357670 2355504 2353338
>> > 2351172 2349006 2346840 2344674 2342508 ...
>> > 20090826 15:15:33| Model: smooth.spline
>> > 20090826 15:15:33| Degrees of freedom: 5
>> > 20090826 15:15:33| Getting algorithm parameters...done
>> > 20090826 15:15:33| Exact fitting of model by incrementally
>> > building the normal equations (X'X = X'y) and then solve it...
>> > 20090826 15:15:33| Get normal equations X'X = X'y...
>> > 20090826 15:15:33| Retrieving cell sequence annotation data file...
>> > Error in list(`source("cnvanalysis_Max_04_HB.R")` = <environment>,
>> > `eval.with.vis(ei, envir)` = <environment>, :
>>
>> > [2009-08-26 15:15:33] Exception: Could not locate a file for this chip
>> > type: GenomeWideSNP_5
>> > at throw(Exception(...))
>> > at throw.default("Could not locate a file for this chip type: ",
>> > paste(c(chipT
>> > at throw("Could not locate a file for this chip type: ",
>> > paste(c(chipType, tag
>> > at method(static, ...)
>> > at AromaCellSequenceFile$byChipType(chipType, ...)
>> > at getAromaCellSequenceFile.AbstractProbeSequenceNormalization(this,
>> > verbose =
>> > at getAromaCellSequenceFile(this, verbose = less(verbose, 20))
>> > at getNormalEquations.LinearModelProbeSequenceNormalization(this, df =
>> > df, cel
>> > at getNormalEquations(this, df = df, cells = cells, ram = ram, verbose =
>> > verbo
>> > at fitOne.LinearModelProbeSequenceNormalization(this, df = df, params =
>> > params
>> > at fitOne(this, df = df, params = params, ram = ram, verbose =
>> > less(verbose, 5
>> > at process.AbstractProbeSequenceNormalization(bpn, verbose = log)
>> > at process(bpn, verbose = log)
>> > at eval.with.vis(expr, envir, enclos)
>> > at eval.with.vis
>> > 20090826 15:15:33| Retrieving cell sequence annotation data
>> > file...done
>> > 20090826 15:15:33| Get normal equations X'X = X'y...done
>> > 20090826 15:15:33| Exact fitting of model by incrementally
>> > building the normal equations (X'X = X'y) and then solve it...done
>> > 20090826 15:15:33| Fitting normalization function for one array...done
>> > 20090826 15:15:33| Fitting model for current array...done
>> > 20090826 15:15:33| Array #1 ('APOC121') of 66...done
>> > 20090826 15:15:33| Path:
>> > probeData/sleData,ACC,ra,-XY,BPN,-XY/GenomeWideSNP_5...done
>> > 20090826 15:15:33| Normalizing 66 arrays...done
>> > 20090826 15:15:33|Normalization data set for probe-sequence effects...done
>> > #######################################
>>
>> > Does anybody know how to fix this problem?
>>
>> > Thanks
>>
>> > Max
> >
>
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