Question: goseq: pwf: Error in if (hi <= low) { : missing value where TRUE/FALSE needed
gravatar for 刘鹏飞
5.7 years ago by
刘鹏飞80 wrote:
Hi, all I am trying to use goseq for RNAseq data analysis of a non-native bacteria, I fetch the genelength data and GO term data by using ensembl Perl API. Differential expression was done by DESeq2. After data run pwf of goseq, error occurred as following: ### Error in if (hi <= low) { : missing value where TRUE/FALSE needed Have any one met this before? How could I solved this problem? Thanks! My workflow were as following ## import the genes ID which I fetch from Ensembl HZ254gene_data <- read.delim("E:/HZ_GO_enrichment/HZ254gene_data.txt", quote="") colnames(HZ254gene_data)[1]="locus_tag" ## get assayed gene vector assayed.genes=HZ254gene_data$locus_tag assayed.genes1=as.vector(assayed.genes) is.vector(assayed.genes1) [1] TRUE head (assayed.genes1) [1] "Mtc_0001" "Mtc_0002" "Mtc_0003" "Mtc_0004" "Mtc_0005" "Mtc_0006" str(assayed.genes1) chr [1:2512] "Mtc_0001" "Mtc_0002" "Mtc_0003" "Mtc_0004" "Mtc_0005" ... ## get gene length data for pwf length=HZ254gene_data$length is.vector(length) [1] TRUE names(length)=assayed.genes1 head(length) Mtc_0001 Mtc_0002 Mtc_0003 Mtc_0004 Mtc_0005 Mtc_0006 768 654 1899 1770 351 654 # str(length) Named int [1:2512] 768 654 1899 1770 351 654 903 72 966 1071 ... - attr(*, "names")= chr [1:2512] "Mtc_0001" "Mtc_0002" "Mtc_0003" "Mtc_0004" ... ##import results from DESeq2 and get the DEgenes HZ254DifList_Mer <- read.delim("E:/HZ_GO_enrichment/HZ254DifList_Mer.txt") de.genes1=as.integer(HZ254DifList_Mer$padj<0.05) ##get the genes for pwf gene.vector=as.integer(de.genes1) names(gene.vector)=assayed.genes1 head(gene.vector) ##import the GO_gene association table from ensembl API HZ254gene_go <- read.delim("E:/HZ_GO_enrichment/HZ254gene_go.txt", quote="") go.terms=HZ254gene_go ## run pwf, pwf=nullp(gene.vector, ##got errors Error in if (hi <= low) { : missing value where TRUE/FALSE needed sessionInfo() R version 3.0.2 (2013-09-25) Platform: x86_64-w64-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=Chinese (Simplified)_People's Republic of China.936 [2] LC_CTYPE=Chinese (Simplified)_People's Republic of China.936 [3] LC_MONETARY=Chinese (Simplified)_People's Republic of China.936 [4] LC_NUMERIC=C [5] LC_TIME=Chinese (Simplified)_People's Republic of China.936 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] goseq_1.14.0 geneLenDataBase_0.99.12 BiasedUrn_1.06.1 [4] BiocInstaller_1.12.0 loaded via a namespace (and not attached): [1] AnnotationDbi_1.24.0 Biobase_2.22.0 BiocGenerics_0.8.0 [4] biomaRt_2.18.0 Biostrings_2.30.1 bitops_1.0-6 [7] BSgenome_1.30.0 DBI_0.2-7 GenomicFeatures_1.14.2 [10] GenomicRanges_1.14.4 grid_3.0.2 IRanges_1.20.6 [13] lattice_0.20-24 Matrix_1.1-2 mgcv_1.7-28 [16] nlme_3.1-113 parallel_3.0.2 RCurl_1.95-4.1 [19] Rsamtools_1.14.3 RSQLite_0.11.4 rtracklayer_1.22.3 [22] stats4_3.0.2 tools_3.0.2 XML_3.98-1.1 [25] XVector_0.2.0 zlibbioc_1.8.0 -- Pengfei Liu, PhD Candidate Lab of Molecular Ecology - Max Planck Partner Group College of Resources and Environmental Sciences China Agricultural University No.2 Yuanmingyuanxilu, Beijing, 100193 P.R. China Tel: +86-10-62731358 Fax: +86-10-62731016 E-mail: [[alternative HTML version deleted]]
rnaseq go goseq deseq2 • 1.0k views
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