On Mon, Jan 26, 2015 at 7:31 AM, Jerry Liu <jerry.liu2...@gmail.com> wrote:
>
> Hello,
>
> I got an error after trying to fit the CBS model:
>
> Error: hgu133aPFAM is defunct. Please use select() if you
> need access to PFAM or PROSITE accessions.
>
> Here are the command I ran:
>
> ds<-doCRMAv2("GSE57277_DLBCL", chipType="Mapping250K_Sty", plm="RmaCnPlm")
> sm<-CbsModel(ds)
> fit(sm, verbose=-10)
>
> I have no clue of how to use select() as per the error message to fix this
> problem. My R session info is at the bottom of the email. Please help, many
> thanks!
This does not an error message for the Aroma Framework, but more
likely something from a Bioconductor package. It's not obvious to me
how that is triggered by the above call. Could you please send what
traceback() outputs immediately after you get the error.
/Henrik
>
> Jerry
>
>
> sessionInfo():
> R version 3.1.1 (2014-07-10)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> 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] stats4 parallel stats graphics grDevices
> [6] utils datasets methods base
>
> other attached packages:
> [1] DNAcopy_1.40.0 preprocessCore_1.28.0
> [3] sfit_0.3.0 aroma.light_2.2.0
> [5] aroma.affymetrix_2.12.0 aroma.core_2.12.1
> [7] R.devices_2.12.0 R.filesets_2.6.0
> [9] R.utils_1.34.0 R.oo_1.18.0
> [11] affxparser_1.38.0 R.methodsS3_1.6.1
> [13] hgu133a.db_3.0.0 org.Hs.eg.db_3.0.0
> [15] RSQLite_1.0.0 DBI_0.3.1
> [17] gage_2.16.0 annotate_1.44.0
> [19] XML_3.98-1.1 AnnotationDbi_1.28.1
> [21] GenomeInfoDb_1.2.3 IRanges_2.0.0
> [23] S4Vectors_0.4.0 hgu133acdf_2.15.0
> [25] affy_1.44.0 Biobase_2.26.0
> [27] BiocGenerics_0.12.1
>
> loaded via a namespace (and not attached):
> [1] affyio_1.34.0 aroma.apd_0.5.0
> [3] base64enc_0.1-2 BiocInstaller_1.16.1
> [5] Biostrings_2.34.0 Cairo_1.5-6
> [7] digest_0.6.4 graph_1.44.0
> [9] httr_0.5 KEGGREST_1.6.1
> [11] matrixStats_0.12.2 png_0.1-7
> [13] PSCBS_0.43.0 R.cache_0.10.0
> [15] R.huge_0.8.0 R.rsp_0.19.0
> [17] splines_3.1.1 stringr_0.6.2
> [19] tools_3.1.1 xtable_1.7-4
> [21] XVector_0.6.0 zlibbioc_1.12.0
>
> --
> --
> 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/.
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