Hi,
something must have going wrong with your intermediate data results
while you tried to use those earlier and incorrect annotation data
files. I recommend that start from scratch by completely deleting:
probeData/Mcels,QN/GenomeWideSNP_6/
plmData/Mcels,QN,RMA,A+B/GenomeWideSNP_6/
and rerun your analysis script, i.e.
library("aroma.affymetrix");
verbose <- Arguments$getVerbose(-8, timestamp=TRUE);
cdf <- AffymetrixCdfFile$byChipType("GenomeWideSNP_6", tags="Full");
csR <- AffymetrixCelSet$byName("Mcels", cdf=cdf);
print(csR);
qn <- QuantileNormalization(csR);
print(qn);
csN <- process(qn, verbose=verbose);
plm <- RmaCnPlm(csN, combineAlleles=TRUE, mergeStrands=TRUE, shift=+300);
print(plm);
fit(plm, verbose=verbose);
ces <- getChipEffectSet(plm);
print(ces);
fln <- FragmentLengthNormalization(ces, target="zero");
print(fln);
cesN <- process(fln, verbose=verbose);
print(cesN);
You can check that your data look alright by doing the following along the way:
plotDensity(csR);
plotDensity(csN);
plotDensity(ces);
plotDensity(cesN);
/Henrik
PS. I've noticed that the code in the CRMAv1 vignette never got
updated and still does quantile normalization (although it writes that
you should really use allelic crosstalk calibration). Sorry about
that - it's been such along time ago CRMAv1 was used. I will try to
fix this. For most people I really recommend to use to new doCRMAv1()
and doCRMAv2() methods, cf. http://aroma-project.org/blocks/
On Mon, Jun 7, 2010 at 10:22 PM, Jack <kangarooj...@gmail.com> wrote:
> Hi Henrik,
>
> I've ran the entirety of the vignette up to the same point (I did
> forget to run the fit(plm, verbose=verbose) and the same error
> persists.
>
> The reason I'm using version 1 is because all we need is the raw copy
> number so we didn't need any of the additional tools/calculations.
>
> traceback()
> 8: throw.Exception(Exception(...))
> 7: throw(Exception(...))
> 6: throw.default("Cannot fit target function to enzyme, because there
> are no (finite) data points that are unique to this enzyme: ",
> ee)
> 5: throw("Cannot fit target function to enzyme, because there are no
> (finite) data points that are unique to this enzyme: ",
> ee)
> 4: getTargetFunctions.FragmentLengthNormalization(this, verbose =
> less(verbose))
> 3: getTargetFunctions(this, verbose = less(verbose))
> 2: process.FragmentLengthNormalization(fln, verbose = verbose)
> 1: process(fln, verbose = verbose)
>
> sessionInfo()
> R version 2.11.1 (2010-05-31)
> powerpc-apple-darwin9.8.0
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods
> base
>
> other attached packages:
> [1] preprocessCore_1.10.0 aroma.affymetrix_1.6.0
> aroma.apd_0.1.7 affxparser_1.20.0 R.huge_0.2.0
> [6] aroma.core_1.6.0 aroma.light_1.16.0
> matrixStats_0.2.1 R.rsp_0.3.6 R.cache_0.3.0
> [11] R.filesets_0.8.1 digest_0.4.2
> R.utils_1.4.0 R.oo_1.7.2 R.methodsS3_1.2.0
>
> loaded via a namespace (and not attached):
> [1] tools_2.11.1
>
> print(ces) yields:
>
> CnChipEffectSet:
> Name: Mcels
> Tags: QN,RMA,A+B
> Path: plmData/Mcels,QN,RMA,A+B/GenomeWideSNP_6
> Platform: Affymetrix
> Chip type: GenomeWideSNP_6,Full,monocell
> Number of arrays: 4
> Names: GM6, GM7, GM8, GM9
> Time period: 2010-06-04 16:10:31 -- 2010-06-04 16:10:36
> Total file size: 107.80MB
> RAM: 0.01MB
> Parameters: (probeModel: chr "pm", mergeStrands: logi TRUE,
> combineAlleles: logi TRUE)
>
> --
> 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 website http://www.aroma-project.org/.
> To post to this group, send email to aroma-affymetrix@googlegroups.com
> To unsubscribe and other options, go to http://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.
You received this message because you are subscribed to the Google Groups
"aroma.affymetrix" group with website http://www.aroma-project.org/.
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