Problem with Total Copy Number Vignette
Jack Yu
I sent an e-mail earlier regarding errors in running the total copy
number vignette, but please disregard that as it turns out it was just
an issue with the annotation files. Sorry for the inconveniences.
However, I've encountered another problem that I'm hoping someone
could help me with.
After running the normalization of the chip effects using:
cesNList[[chipType]] <- process(fln, verbose=verbose)
I encountered the error of:
Error in list(`process(fln, verbose = verbose)` = <environment>,
`process.FragmentLengthNormalization(fln, verbose = verbose)` =
<environment>, :
[2010-06-07 09:34:07] Exception: Cannot fit target function to enzyme,
because there are no (finite) data points that are unique to this
enzyme: 1
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] aroma.affymetrix_1.6.0 aroma.apd_0.1.7 affxparser_1.20.0
R.huge_0.2.0 aroma.core_1.6.0
[6] aroma.light_1.16.0 matrixStats_0.2.1 R.rsp_0.3.6
R.cache_0.3.0 R.filesets_0.8.1
[11] digest_0.4.2 R.utils_1.4.0 R.oo_1.7.2
R.methodsS3_1.2.0
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)
Thanks in advance,
Jack
--
Jack Y. Yu
Washington University in St.Louis
(505) 920-0701
Henrik Bengtsson
On Mon, Jun 7, 2010 at 3:36 PM, Jack Yu <j.y...@gmail.com> wrote:
> Hello,
>
> I sent an e-mail earlier regarding errors in running the total copy
> number vignette, but please disregard that as it turns out it was just
> an issue with the annotation files. Sorry for the inconveniences.
Good. I've just send a message to that thread/discussion ('Error
during Total copy number analysis using CRMA v1', June 4, 2010)
closing it. That way anyone reading the forum archives can see it was
solved. In the future, please always try to reply to original thread
saying that it's been solved or not.
> However, I've encountered another problem that I'm hoping someone
> could help me with.
>
> After running the normalization of the chip effects using:
>
> cesNList[[chipType]] <- process(fln, verbose=verbose)
>
> I encountered the error of:
>
> Error in list(`process(fln, verbose = verbose)` = <environment>,
> `process.FragmentLengthNormalization(fln, verbose = verbose)` =
> <environment>, :
>
> [2010-06-07 09:34:07] Exception: Cannot fit target function to enzyme,
> because there are no (finite) data points that are unique to this
> enzyme: 1
Are you following the same vignette ('Total copy number analysis using
CRMA v1 (10K, 100K, 500K)') as you did your previous thread? Then my
best guess is that you forgot to do:
fit(plm, verbose=verbose);
before moving on to the PCR fragment length normalization. If that
does not help, let me know what the output of:
ces <- getChipEffectSet(plm);
print(ces);
More importantly, is there a reason why you want to use CRMAv1 and not
CRMAv2? Note that the latter is recommended for GenomeWideSNP_6 data
sets. To use CRMAv2, see vignette 'Estimation of total copy numbers
using the CRMA v2 method (10K-GWS6)'
[http://aroma-project.org/vignettes/CRMAv2].
...or even easier, just use the new doCRMAv1() or doCRMAv2(), cf.
http://aroma-project.org/blocks
/Henrik
> --
> 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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>
Jack
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)
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:
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)
Henrik Bengtsson
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/