Question

FourCSeq problem with getZScores

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Entering edit mode

a.chesi • 0

@achesi-8666

Last seen 9.3 years ago

United States

Hi,

I am using FourCseq with one 4C experiment with 2 biological replicates.

When I run:

fcf <- getZScores(fc)

I get the following error:

Error in getZScores(fc) : could not find function "getVST".

Could you please help me with this?

R version 3.2.1 (2015-06-18) -- "World-Famous Astronaut"

Bioconductor version 3.1 (BiocInstaller 1.18.4), ?biocLite for help

Warning message:

package ‘RcppArmadillo’ was built under R version 3.2.2

> sessionInfo()
R version 3.2.1 (2015-06-18)
Platform: x86_64-apple-darwin10.8.0 (64-bit)
Running under: OS X 10.8.5 (Mountain Lion)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] splines stats4 parallel stats graphics grDevices utils datasets methods base

other attached packages:
[1] FourCSeq_1.2.0 LSD_3.0 DESeq2_1.8.1 RcppArmadillo_0.5.300.4 Rcpp_0.12.0
[6] ggplot2_1.0.1 GenomicRanges_1.20.5 GenomeInfoDb_1.4.1 IRanges_2.2.6 S4Vectors_0.6.3
[11] BiocGenerics_0.14.0

loaded via a namespace (and not attached):
[1] locfit_1.5-9.1 biovizBase_1.16.0 lattice_0.20-33 gtools_3.5.0 Rsamtools_1.20.4
[6] Biostrings_2.36.2 digest_0.6.8 plyr_1.8.3 futile.options_1.0.0 acepack_1.3-3.3
[11] RSQLite_1.0.0 zlibbioc_1.14.0 GenomicFeatures_1.20.1 annotate_1.46.1 rpart_4.1-10
[16] Matrix_1.2-2 ggbio_1.16.1 proto_0.3-10 BiocParallel_1.2.19 geneplotter_1.46.0
[21] stringr_1.0.0 foreign_0.8-65 RCurl_1.95-4.7 biomaRt_2.24.0 munsell_0.4.2
[26] rtracklayer_1.28.7 nnet_7.3-10 gridExtra_2.0.0 Hmisc_3.16-0 XML_3.98-1.3
[31] reshape_0.8.5 GenomicAlignments_1.4.1 MASS_7.3-43 bitops_1.0-6 RBGL_1.44.0
[36] grid_3.2.1 xtable_1.7-4 GGally_0.5.0 gtable_0.1.2 DBI_0.3.1
[41] magrittr_1.5 scales_0.2.5 graph_1.46.0 stringi_0.5-5 XVector_0.8.0
[46] reshape2_1.4.1 genefilter_1.50.0 latticeExtra_0.6-26 futile.logger_1.4.1 Formula_1.2-1
[51] lambda.r_1.1.7 RColorBrewer_1.1-2 tools_3.2.1 dichromat_2.0-0 OrganismDbi_1.10.0
[56] BSgenome_1.36.3 Biobase_2.28.0 survival_2.38-3 AnnotationDbi_1.30.1 colorspace_1.2-6
[61] cluster_2.0.3 fda_2.4.4 VariantAnnotation_1.14.6
> traceback()
1: getZScores(fc)

FourCSeq • 1.3k views

ADD COMMENT • link updated 9.2 years ago by felix.klein ▴ 150 • written 9.2 years ago by a.chesi • 0

score 0 · Answer 1 · 2015-08-31

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Entering edit mode

felix.klein ▴ 150

@felixklein-6900

Last seen 6.4 years ago

Germany

Hello Alessandra, I cannot reproduce your error. Could you please tell me how you call the getZScore function? From the error it seems like you are not calling the function of the package itself. getVST is a function of the FourCSeq package that is not exported. Therefore you get the error message that the function getVST can not be found, if you are calling the getZScore function outside the FourCSeq Namespace. If you have written your modifized getZScore function you have to replace getVST by FourCSeq:::getVST. This hopefully resolves your problem. Best regards, Felix

ADD COMMENT • link 9.2 years ago felix.klein ▴ 150

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Entering edit mode

Hi Felix, thank you very much, this solves my problem. I was able to solve the problem by opening a fresh R project. Best, Alessandra On Aug 31, 2015, at 2:38 PM, "felix.klein [bioc]" <noreply@bioconductor.org> wrote: > Activity on a post you are following on support.bioconductor.org > User felix.klein wrote Answer: FourCSeq problem with getZScores: > > > Hello Alessandra, I cannot reproduce your error. Could you please tell me how you call the getZScore function? From the error it seems like you are not calling the function of the package itself. getVST is a function of the FourCSeq package that is not exported. Therefore you get the error message that the function getVST can not be found, if you are calling the getZScore function outside the FourCSeq Namespace. If you have written your modifized getZScore function you have to replace getVST by FourCSeq:::getVST. This hopefully resolves your problem. Best regards, Felix > > Post tags: FourCSeq > > You may reply via email or visit A: FourCSeq problem with getZScores >

ADD REPLY • link 9.2 years ago a.chesi • 0