Filtering DESeq2 results for | LFC | > 1 genes
1
0
Entering edit mode
ayy2110 • 0
@50930c2c
Last seen 5 weeks ago
United States
res_LFC <- res[which(abs(res$log2FoldChange) > 1)]
Error: subscript contains out-of-bounds indices

I am performing differential gene expression analysis using DESeq2. I am able to successfully run deseq2, and I generate a results table that i called res. i want to filter res for genes with |LFC| > 1, and so I wrote the above code. I dont understand why i obtain the error message though. can anyone provide some insight?

R version 4.0.3 (2020-10-10) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 17763)

Matrix products: default

locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252

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

loaded via a namespace (and not attached): [1] MatrixGenerics_1.2.1 Biobase_2.50.0 httr_1.4.2 bit64_4.0.5
[5] splines_4.0.3 assertthat_0.2.1 askpass_1.1 stats4_4.0.3
[9] BiocFileCache_1.14.0 blob_1.2.1 Rsamtools_2.6.0 GenomeInfoDbData_1.2.4
[13] progress_1.2.2 pillar_1.6.1 RSQLite_2.2.7 lattice_0.20-44
[17] glue_1.4.2 GenomicRanges_1.42.0 RColorBrewer_1.1-2 XVector_0.30.0
[21] colorspace_2.0-1 Matrix_1.2-18 DESeq2_1.30.1 XML_3.99-0.6
[25] pkgconfig_2.0.3 biomaRt_2.46.3 genefilter_1.72.1 zlibbioc_1.36.0
[29] purrr_0.3.4 xtable_1.8-4 scales_1.1.1 BiocParallel_1.24.1
[33] tibble_3.1.1 openssl_1.4.4 annotate_1.68.0 generics_0.1.0
[37] IRanges_2.24.1 ggplot2_3.3.3 ellipsis_0.3.2 cachem_1.0.4
[41] SummarizedExperiment_1.20.0 GenomicFeatures_1.42.3 BiocGenerics_0.36.1 survival_3.2-11
[45] magrittr_2.0.1 crayon_1.4.1 memoise_2.0.0 fansi_0.4.2
[49] xml2_1.3.2 tools_4.0.3 prettyunits_1.1.1 hms_1.1.0
[53] lifecycle_1.0.0 matrixStats_0.58.0 stringr_1.4.0 S4Vectors_0.28.1
[57] munsell_0.5.0 locfit_1.5-9.4 DelayedArray_0.16.3 AnnotationDbi_1.52.0
[61] Biostrings_2.58.0 compiler_4.0.3 GenomeInfoDb_1.26.7 rlang_0.4.11
[65] grid_4.0.3 RCurl_1.98-1.3 rstudioapi_0.13 rappdirs_0.3.3
[69] bitops_1.0-7 gtable_0.3.0 curl_4.3.1 DBI_1.1.1
[73] R6_2.5.0 GenomicAlignments_1.26.0 rtracklayer_1.49.5 dplyr_1.0.5
[77] fastmap_1.1.0 bit_4.0.4 utf8_1.2.1 stringi_1.5.3
[81] parallel_4.0.3 Rcpp_1.0.6 vctrs_0.3.8 geneplotter_1.68.0
[85] dbplyr_2.1.1 tidyselect_1.1.1
RNAseq LFC DEseq • 77 views
ADD COMMENT
0
Entering edit mode
ayy2110 • 0
@50930c2c
Last seen 5 weeks ago
United States

turns out i was missing a comma!

res_LFC <- res[which(abs(res$log2FoldChange) > 1),]
ADD COMMENT

Login before adding your answer.

Traffic: 347 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6