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  • CummeRbund: Warnings, not averaging correct samples together

    Hi, I'm reanalyzing some data from a few years ago. When I put it back into readCufflinks() I get the following warnings after some other problem solving:

    >cuff_data<- readCufflinks('diff',rebuild=T)

    50X:
    >In result_fetch(res@ptr, n = n) :
    Don't need to call dbFetch() for statements, only for queries

    It seems to make the database otherwise, but when I look at gene expression graphs, it has columns labeled for one of each of my wild-type controls with error bars, but no other genotypes (3 genotypes x3 replicates set up). What did I do wrong and how do I fix it?

    >sessionInfo()
    R version 3.5.1 (2018-07-02)
    Platform: x86_64-apple-darwin15.6.0 (64-bit)
    Running under: macOS High Sierra 10.13.6

    Matrix products: default
    BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
    LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib

    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] grid stats4 parallel stats graphics grDevices utils datasets methods base

    other attached packages:
    [1] cummeRbund_2.22.0 Gviz_1.24.0 rtracklayer_1.40.6 GenomicRanges_1.32.7 GenomeInfoDb_1.16.0
    [6] IRanges_2.14.12 S4Vectors_0.18.3 fastcluster_1.1.25 reshape2_1.4.3 ggplot2_3.0.0
    [11] RSQLite_2.1.1 BiocGenerics_0.26.0

    loaded via a namespace (and not attached):
    [1] ProtGenerics_1.12.0 bitops_1.0-6 matrixStats_0.54.0 bit64_0.9-7
    [5] RColorBrewer_1.1-2 progress_1.2.0 httr_1.3.1 tools_3.5.1
    [9] backports_1.1.2 R6_2.2.2 rpart_4.1-13 Hmisc_4.1-1
    [13] DBI_1.0.0 lazyeval_0.2.1 colorspace_1.3-2 nnet_7.3-12
    [17] withr_2.1.2 tidyselect_0.2.4 gridExtra_2.3 prettyunits_1.0.2
    [21] curl_3.2 bit_1.1-14 compiler_3.5.1 Biobase_2.40.0
    [25] htmlTable_1.12 DelayedArray_0.6.6 scales_1.0.0 checkmate_1.8.5
    [29] stringr_1.3.1 digest_0.6.17 Rsamtools_1.32.3 foreign_0.8-71
    [33] XVector_0.20.0 base64enc_0.1-3 dichromat_2.0-0 pkgconfig_2.0.2
    [37] htmltools_0.3.6 ensembldb_2.4.1 BSgenome_1.48.0 htmlwidgets_1.2
    [41] rlang_0.2.2 rstudioapi_0.7 bindr_0.1.1 BiocParallel_1.14.2
    [45] acepack_1.4.1 dplyr_0.7.6 VariantAnnotation_1.26.1 RCurl_1.95-4.11
    [49] magrittr_1.5 GenomeInfoDbData_1.1.0 Formula_1.2-3 Matrix_1.2-14
    [53] Rcpp_0.12.18 munsell_0.5.0 stringi_1.2.4 yaml_2.2.0
    [57] SummarizedExperiment_1.10.1 zlibbioc_1.26.0 plyr_1.8.4 blob_1.1.1
    [61] crayon_1.3.4 lattice_0.20-35 Biostrings_2.48.0 splines_3.5.1
    [65] GenomicFeatures_1.32.2 hms_0.4.2 knitr_1.20 pillar_1.3.0
    [69] biomaRt_2.36.1 XML_3.98-1.16 glue_1.3.0 biovizBase_1.28.2
    [73] latticeExtra_0.6-28 data.table_1.11.4 gtable_0.2.0 purrr_0.2.5
    [77] assertthat_0.2.0 AnnotationFilter_1.4.0 survival_2.42-6 tibble_1.4.2
    [81] GenomicAlignments_1.16.0 AnnotationDbi_1.42.1 memoise_1.1.0 bindrcpp_0.2.2
    [85] cluster_2.0.7-1

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