Exception: Could not locate a file for this chip type: GenomeWideSNP_5

[Max Moldovan]

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

[Henrik Bengtsson]

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-total-copy-numbers-using-the-crma-v2-method

which helps you make sure you got everything setup before starting.

Cheers,

Henrik

[Max Moldovan]

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,
>

[Henrik Bengtsson]

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