I've also encoundered another problem, this time I believe related to a
change the the frma package which requires a corresponding change in the
frmaTools package. Apparently frma has added a check for equality of
probe names in various places, and frmaTools does not store these names,
which means that the current version of frma will reject any vectors
generated by the current version of frmaTools with the following error:
> eset <- frma(affy[,1:3] , input.vecs=myFrmaToolsVecs)
Error in frmaAffyBatch(object, background, normalize, summarize,
input.vecs, :
Mismatch between pmindex(object) and names of input.vecs and unable
to create unique mapping.
> traceback()
3: stop("Mismatch between pmindex(object) and names of input.vecs and
unable to create unique mapping.")
2: frmaAffyBatch(object, background, normalize, summarize, input.vecs,
output.param, verbose)
1: frma(affy[, 1:3], input.vecs = myFrmaToolsVecs)
> sessionInfo()
R version 3.2.0 (2015-04-16)
Platform: x86_64-unknown-linux-gnu (64-bit)
Running under: Ubuntu 15.04
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] grDevices datasets parallel graphics stats4 stats utils
[8] methods base
other attached packages:
[1] frmaTools_1.20.0
[2] hgu133afrmavecs_1.5.0
[3] hthgu133pluspmcdf_2.16.0
[4] DSalomon.PAX.hthgu133pluspmfrmavecs_0.1
[5] frma_1.20.0
[6] affy_1.46.1
[7] Biobase_2.28.0
[8] openxlsx_2.5.10
[9] foreach_1.4.2
[10] plyr_1.8.3
[11] stringr_1.0.0
[12] IRanges_2.2.4
[13] ggplot2_1.0.1
[14] S4Vectors_0.6.0
[15] BiocGenerics_0.14.0
[16] BiocInstaller_1.18.3
loaded via a namespace (and not attached):
[1] Rcpp_0.11.6 compiler_3.2.0 GenomeInfoDb_1.4.1
[4] XVector_0.8.0 iterators_1.0.7 tools_3.2.0
[7] zlibbioc_1.14.0 digest_0.6.8 bit_1.1-12
[10] RSQLite_1.0.0 preprocessCore_1.30.0 gtable_0.1.2
[13] ff_2.2-13 DBI_0.3.1 proto_0.3-10
[16] affxparser_1.40.0 Biostrings_2.36.1 grid_3.2.0
[19] AnnotationDbi_1.30.1 oligo_1.32.0 reshape2_1.4.1
[22] magrittr_1.5 splines_3.2.0 scales_0.2.5
[25] codetools_0.2-11 oligoClasses_1.30.0 MASS_7.3-41
[28] GenomicRanges_1.20.5 colorspace_1.2-6 stringi_0.5-2
[31] munsell_0.4.2 affyio_1.36.0
On 07/07/2015 06:52 AM, Matthew McCall wrote:
Ryan,
Thanks for pointing these out. I'll look into them soon, but I imagine
your assessment is correct.
Best,
Matt
On Mon, Jul 6, 2015 at 5:42 PM, Ryan C. Thompson <r...@thompsonclan.org
<mailto:r...@thompsonclan.org>> wrote:
I also discovered another apparent bug later in the same function.
The second to last line of makeVectorsAffyBatch is
vers <- ifelse(!is.null(cdfname),
as.character(packageVersion(cdfname)), "")
If cdfname is NULL, this line will throw an error because the
second argument to ifelse will have length zero and "ifelse" does
NOT do lazy evaluation.
On 07/06/2015 12:21 PM, Ryan C. Thompson wrote:
Hello,
I just encountered a bug in frmaTools that makes it impossible
to use on certain array platforms. The following lines in
makeVectorsAffyBatch fail on an AffyBatch object on the
hthgu133pluspm platform:
pms <- pm(object)
pns <- probeNames(object)
pmi <- unlist(pmindex(object))
if (!identical(as.character(pmi), rownames(pms)))
stop("Mismatch between pmindex and rownames of pms")
I isolated the problem to five probes:
> i <- which(as.character(pmi) != rownames(pms))
> pmi[i]
1564498_PM_at9 205398_PM_s_at8 217695_PM_x_at7
223446_PM_s_at7 237802_PM_at3
3e+05 5e+05 2e+05 1e+05 4e+05
> rownames(pms)[i]
[1] "300000" "500000" "200000" "100000" "400000"
> as.character(pmi)[i]
[1] "3e+05" "5e+05" "2e+05" "1e+05" "4e+05"
As you can see, the problem is that as.character will happily
use scientific notation when it feels like it, which then
fails a test for string equality. I believe the solution is to
replace that test with:
all(sprintf("%i", pmi) == rownames(pms))
-Ryan
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