SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Correct way of merging samples for father, mother, child trio variant calling Eurioste Bioinformatics 1 07-05-2017 08:01 PM
Warnings using Galaxy and local CummeRbund masefieldcourt Bioinformatics 1 04-12-2017 06:23 AM
How to name samples in CummeRbund? veber Bioinformatics 4 12-08-2014 04:10 AM
cummerBund -> Doesn't see my samples madkitty Bioinformatics 1 02-18-2014 05:02 AM
DBI and RSQLite Errors plus other Warnings when Installing CummeRbund jmwhitha Bioinformatics 21 06-22-2013 07:41 PM

Reply
 
Thread Tools
Old 09-26-2018, 08:12 PM   #1
skmotay
Member
 
Location: MN

Join Date: Oct 2014
Posts: 29
Default 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([email protected], 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
skmotay is offline   Reply With Quote
Reply

Tags
cuff links, cummerbund, r programming

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 04:58 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO