Hi Gene Tastic,
On Mon, Aug 16, 2010 at 2:57 PM, Gene <genetas...@gmail.com> wrote:
> I'm getting the dreaded "Exception: Cannot fit target function to
> enzyme, because there are no (finite) data points that are unique to
> this enzyme" error, that has popped up a number of times on this board
> previously. However the usual problem, that fit(plm) wasn't run isn't
> the case here, so I'm stuck.
Thanks for checking this.
Can you update aroma.affymetrix to the most recent version (1.7.0):
source("http://aroma-project.org/hbLite.R";);
hbInstall("aroma.affymetrix");
and then paste the output of
verbose <- Arguments$getVerbose(-8)
ds <- lapply(chipTypes, function(x) {
doCRMAv2("gsk", chipType=x, plm="RmaCnPlm", verbose=verbose)
})
?
Thanks,
Pierre
> I've tried to run this the more
> automated way:
>
>
> chipTypes <- c("Mapping250K_Sty", "Mapping250K_Nsp")
> name <- 'gsk'
> ds <- lapply(chipTypes, function(x)
> doCRMAv2("gsk",chipType=x,verbose=-1, plm="RmaCnPlm"))
>
> or the more manual way:
>
> css <- lapply(chipTypes, function(x) AffymetrixCelSet$byName(name,
> chipType=x, verbose=T))
> css <- lapply(css, function(x) extract(x, !isDuplicated(x)))
> print(css)
> accs <- lapply(css, AllelicCrosstalkCalibration, model="CRMAv2")
> csCs <- lapply(accs, process, verbose=verbose)
> print(csCs)
> plms <- lapply(csCs, RmaCnPlm, mergeStrands=TRUE, combineAlleles=TRUE)
> print(plms)
> lapply(plms, fit, verbose=T)
> cess <- lapply(plms, getChipEffectSet)
> flns <- lapply(cess, FragmentLengthNormalization)
> cesns <- lapply(flns, process, verobse=-1)
>
> but either way I end up with something like this:
>
>
> Error in list(`lapply(flns, process, verobse = -1)` = <environment>,
> `lapply.default(flns, process, verobse = -1)` = <environment>, :
>
> [2010-08-16 14:21:06] Exception: Cannot fit target 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 target function to enzyme, because
> there are no (
> at throw("Cannot fit target function to enzyme, because there are no
> (finite)
> at getTargetFunctions.FragmentLengthNormalization(this, verbose =
> less(verbose
> at getTargetFunctions(this, verbose = less(verbose))
> at process.FragmentLengthNormalization(X[[1]], ...)
> at FUN(X[[1]], ...)
> at lapply.default(flns, process, verobse = -1)
> at lapply(flns, process, verobse = -1)
>
>
> Here is the output of sessionInfo():
>
>
> R version 2.11.1 (2010-05-31)
> x86_64-apple-darwin9.8.0
>
> locale:
> [1] C
>
> attached base packages:
> [1] stats graphics grDevices datasets utils methods
> base
>
> other attached packages:
> [1] preprocessCore_1.10.0 aroma.affymetrix_1.6.0
> aroma.apd_0.1.7
> [4] affxparser_1.20.0 R.huge_0.2.0
> aroma.core_1.6.0
> [7] matrixStats_0.2.1 R.rsp_0.3.6
> R.cache_0.3.0
> [10] R.filesets_0.8.2 digest_0.4.2
> aroma.light_1.16.0
> [13] R.utils_1.4.3 R.oo_1.7.3
> R.methodsS3_1.2.0
>
> loaded via a namespace (and not attached):
> [1] tools_2.11.1
> Warning message:
> 'DESCRIPTION' file has 'Encoding' field and re-encoding is not
> possible
>
>
> Any advice would be greatly appreciated!
>
>
> Thanks
> Gene
>
> --
> 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.
>
>
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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
"aroma.affymetrix" group with website http://www.aroma-project.org/.
To post to this group, send email to aroma-affymetrix@googlegroups.com
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