Hi! I'm following this guide to analyze the raw data from this study (https://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-18670/).
I arrived at the "11.4 Adding more annotation" part, and tried running:
> anncols <- aaf.handler()[c(1:2,9:12)]
> atab <- aafTableAnn(T2$sym, "hgu133plus2.db", anncols)
Error in .checkKeysAreWellFormed(keys) :
keys must be supplied in a character vector with no NAs
So I removed the NA annotated probes with:
> T3 <- T2[complete.cases(T2[ , 2:3]), ]
And then:
> atab <- aafTableAnn(T3$sym, "hgu133plus2.db", anncols)
Error in .checkKeysAreWellFormed(keys) :
keys must be supplied in a character vector with no NAs
> T3$sym
[1] NTPCR LSM5 FAM122A RSAD1
[5] NAA35 CDCA7L C12orf29 UFM1
[9] NADK CFAP20 SH2D1B SLC30A5
[13] DIPK1A PYROXD1 PPP6C ARMC1
[17] FAM220A VPS33B CD3G ATG5
[21] ZBED4 LANCL1 RLIM ELAC1
[25] SRRD GMEB1 ASH1L-AS1 LBH
[29] PIK3R4 ZXDB FGFBP2 CCND2
[33] HSPA13 RPRD1B CHORDC1 TMEM260
[37] GUF1 RTL6 DIPK1A CA5BP1
[41] AASDH RBM8A RBM15B RP9
[45] MAP3K1 ERVH-6 TMPO USP1
[49] ABCC4 HIBADH EEF1AKNMT ZNF318
[53] DDX11L2 MAN1A2 ZNF449 LYRM7
[57] KLHL24 INIP LRRC40 PUS3
[61] SLC38A1 ADGRG5 CCND2 ARIH2
[65] TMX1 SLC25A36 SMAD7 ING3
[69] CLPX EMSY CDC40 MTO1
[73] RNF125 MIA3 ADRB1 PDCD4-AS1
[77] SRP72 N4BP2L2 ASPHD2 RFC3
[81] JCHAIN GOSR2 KLRF1 MAGED1
[85] CDK9 SIKE1 PET117 RBM25
[89] JAZF1 PDGFD MTF2 TCFL5
[93] PLPBP HACE1 CEP120 DNAJB14
[97] CDC73 TMEM185B TENT4B TMEM135
[101] TNRC6C-AS1 GABPB2 SFMBT1 PRMT5
[105] HOPX MTO1 LACTB CYP4V2
[109] PCM1 TDP1 DYRK2 SART3
[113] SEPT6 PLEKHG2 DCLRE1C MTO1
[117] MXRA7 ZFP90 SNX4 PDSS2
[121] MTCH2 RORA RBM7 GORASP2
[125] SNRPA1 MOSPD1 TRIM14 PAICS
[129] IFT122 TESK2 SHQ1 FBXL12
[133] TMEM161B CNIH1 TMEM33 KIAA0232
[137] ANAPC16 VPS33B RAD17 ALDH5A1
[141] TRAPPC11 FBXO21 FLT3LG BRD3OS
[145] ATG2B MFN1 UBLCP1 CD247
[149] CD2 GSR UEVLD SYNE2
[153] FBXO4 KPNA1 LOC285819 STRN
[157] TUBGCP3 PEX13 ABHD15 METTL4
[161] UHMK1 SEPHS1 ZNF550 OSBPL5
[165] ATP6V1E2 SLCO4C1 EFL1 ADPRM
[169] DHX36 ZNF322 GZMA GNLY
[173] HACD2
168 Levels: AASDH ABCC4 ABHD15 ADGRG5 ... ZXDB
Can't tell what's wrong, I believe all NA inputs were removed, so maybe I altered T3 and can no longer be used by aafTableAnn?
Thank you very much for your time.
> sessionInfo()
R version 3.5.2 (2018-12-20)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.1 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=es_AR.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=es_AR.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=es_AR.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=es_AR.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats4 parallel stats graphics grDevices utils
[7] datasets methods base
other attached packages:
[1] annaffy_1.54.0 KEGG.db_3.2.3
[3] GO.db_3.7.0 hgu133plus2.db_3.2.3
[5] affycoretools_1.54.0 annotate_1.60.0
[7] XML_3.98-1.16 org.Hs.eg.db_3.7.0
[9] AnnotationDbi_1.44.0 dplyr_0.7.8
[11] limma_3.38.3 pd.hg.u133.plus.2_3.12.0
[13] DBI_1.0.0 RSQLite_2.1.1
[15] oligo_1.46.0 Biostrings_2.50.2
[17] XVector_0.22.0 IRanges_2.16.0
[19] S4Vectors_0.20.1 Biobase_2.42.0
[21] oligoClasses_1.44.0 BiocGenerics_0.28.0
[23] BiocManager_1.30.4
loaded via a namespace (and not attached):
[1] backports_1.1.3 GOstats_2.48.0
[3] Hmisc_4.1-1 plyr_1.8.4
[5] lazyeval_0.2.1 GSEABase_1.44.0
[7] splines_3.5.2 BiocParallel_1.16.5
[9] GenomeInfoDb_1.18.1 ggplot2_3.1.0
[11] digest_0.6.18 foreach_1.4.4
[13] ensembldb_2.6.3 htmltools_0.3.6
[15] gdata_2.18.0 magrittr_1.5
[17] checkmate_1.9.1 memoise_1.1.0
[19] BSgenome_1.50.0 cluster_2.0.7-1
[21] gcrma_2.54.0 matrixStats_0.54.0
[23] R.utils_2.7.0 ggbio_1.30.0
[25] prettyunits_1.0.2 colorspace_1.4-0
[27] blob_1.1.1 xfun_0.4
[29] crayon_1.3.4 RCurl_1.95-4.11
[31] graph_1.60.0 genefilter_1.64.0
[33] bindr_0.1.1 survival_2.43-3
[35] VariantAnnotation_1.28.8 iterators_1.0.10
[37] glue_1.3.0 gtable_0.2.0
[39] zlibbioc_1.28.0 DelayedArray_0.8.0
[41] Rgraphviz_2.26.0 scales_1.0.0
[43] GGally_1.4.0 edgeR_3.24.3
[45] Rcpp_1.0.0 xtable_1.8-3
[47] progress_1.2.0 htmlTable_1.13.1
[49] foreign_0.8-71 bit_1.1-14
[51] OrganismDbi_1.24.0 preprocessCore_1.44.0
[53] Formula_1.2-3 AnnotationForge_1.24.0
[55] htmlwidgets_1.3 httr_1.4.0
[57] gplots_3.0.1 RColorBrewer_1.1-2
[59] acepack_1.4.1 ff_2.2-14
[61] pkgconfig_2.0.2 reshape_0.8.8
[63] R.methodsS3_1.7.1 nnet_7.3-12
[65] locfit_1.5-9.1 tidyselect_0.2.5
[67] rlang_0.3.1 reshape2_1.4.3
[69] munsell_0.5.0 tools_3.5.2
[71] stringr_1.3.1 knitr_1.21
[73] bit64_0.9-7 caTools_1.17.1.1
[75] purrr_0.2.5 AnnotationFilter_1.6.0
[77] bindrcpp_0.2.2 RBGL_1.58.1
[79] R.oo_1.22.0 biomaRt_2.38.0
[81] compiler_3.5.2 rstudioapi_0.9.0
[83] curl_3.3 affyio_1.52.0
[85] PFAM.db_3.7.0 tibble_2.0.1
[87] geneplotter_1.60.0 stringi_1.2.4
[89] GenomicFeatures_1.34.1 lattice_0.20-38
[91] ProtGenerics_1.14.0 Matrix_1.2-15
[93] pillar_1.3.1 data.table_1.12.0
[95] bitops_1.0-6 rtracklayer_1.42.1
[97] GenomicRanges_1.34.0 R6_2.3.0
[99] latticeExtra_0.6-28 affy_1.60.0
[101] hwriter_1.3.2 KernSmooth_2.23-15
[103] gridExtra_2.3 affxparser_1.54.0
[105] codetools_0.2-16 dichromat_2.0-0
[107] gtools_3.8.1 assertthat_0.2.0
[109] SummarizedExperiment_1.12.0 DESeq2_1.22.2
[111] Category_2.48.0 ReportingTools_2.22.1
[113] GenomicAlignments_1.18.1 Rsamtools_1.34.0
[115] GenomeInfoDbData_1.2.0 hms_0.4.2
[117] grid_3.5.2 rpart_4.1-13
[119] biovizBase_1.30.1 base64enc_0.1-3
Thank you very much!