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. 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.
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/
