Problem with R command during DE Analysis
Issue #104
closed
Hi,
My name is Anna and I am trying to run the whole pipeline on test data you have in example file, at once but its giving me following error,
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miARma, miRNA and RNASeq Multiprocess Analysis
miARma v 1.7.2 (Dec-2017)
Created at Computational Biology and Bioinformatics Group (CbBio)
Institute of Biomedicine of Seville. IBIS (Spain)
Modified and Updated at Bioinformatics Unit at IPBLN-CSIC
Institue for Parasitology and Biomedicine Lopez-Neyra (IPBLN-CSIC).
Granada (Spain)
Copyright (c) 2017 IBIS & IPBLN. All rights reserved.
mail : miARma-devel@cbbio.es
[Sun Feb 4 00:31:08 2018] Starting a miARma analysis for miRNA [Sun Feb 4 00:31:08 2018] Checking provided parameters for: Quality,Adapter,Aligner,ReadCount,DEAnalysis,TargetPrediction. [Sun Feb 4 00:31:08 2018] All parameters are correct. [Sun Feb 4 00:31:08 2018] Starting Quality Analysis. [Sun Feb 4 00:31:33 2018] Quality Analysis finished. [Sun Feb 4 00:31:33 2018] Checking if files in folder: "Examples/basic_examples/miRNAs/reads/" are in the correct fastq format. [Sun Feb 4 00:31:34 2018] Starting a Adapter removal analysis [Sun Feb 4 00:33:59 2018] Adapter Analysis finished. [Sun Feb 4 00:33:59 2018] Starting a Post Quality Analysis [Sun Feb 4 00:34:17 2018] Post Quality Analysis finished. [Sun Feb 4 00:34:17 2018] Starting a "Bowtie1" Alignment Analysis [Sun Feb 4 00:37:47 2018] "Bowtie1" Alignment Analysis finished [Sun Feb 4 00:37:47 2018] Starting a Readcount Analysis [Sun Feb 4 00:37:58 2018] Readcount Analysis finished. [Sun Feb 4 00:37:58 2018] Starting a differential expression analysis using EdgeR software(s) Problem while running this R command: print(resultsfiles)
Error: print(resultsfiles) : object 'resultsfiles' not found Execution halted
Comments (19)
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Hi Eduardo,
What do this mean, (When installing Biocondfutor, you have also to select the personal library folder (when asked). Did you follow these steps?), while installation they said either I will use personal library as the default one was not writable and I pressed Y.
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Hi Eduardo,
I installed Bioconductor but it is still giving me the same error.
print(resultsfiles)
Error: print(resultsfiles) : object 'resultsfiles' not found Execution halted
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Could you try the following ?
1) Enter in a R session (un Mac and Linux you only hace to write R and press enter)
2) Load de bioClite tool in R executing:
source("https://bioconductor.org/biocLite.R")3) Try to install a programm in bioconcuctor, for example edgeR:
biocLite("edgeR")Please let me know what do you see in your terminal
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- attached test
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I attached the text file test which i saw after doing as you mentioned
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Thanks, this helped a lot. I see that you are using the personal folder (installing to /home/eymann/R/x86_64-pc-linux-gnu-library/3.2/) ...
So we move to the next question .... could you attach both log files ? (one should be called something like miARma_log_xxxx.log and the other miARma_stat_xxx.log). Both are placed in the folder you elect in the ini file (value output_dir).
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- attached miARma_stat.24283.log
- attached miARma_logfile.24283.log
These are 2 files generated
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Hi again, pease enter in /home/eymann/Documents/Tools/cbbio/ and execute R. Inside the R console, please write the following three commands:
source("./lib/CbBio/RNASeq/R-Scripts/QC_EdgeR.R") setwd("/home/eymann/Documents/Tools/cbbio/Examples/basic_examples/miRNAs/Known_miRNAs/results/Readcount_results") QC_EdgeR(projectdir="/home/eymann/Documents/Tools/cbbio/Examples/basic_examples/miRNAs/Known_miRNAs/results",dir="/home/eymann/Documents/Tools/cbbio/Examples/basic_examples/miRNAs/Known_miRNAs/results/Readcount_results", file="cut_bw1-ReadCount.tab", targetfile="/home/eymann/Documents/Tools/cbbio/Examples/basic_examples/miRNAs/data/targets.txt", label="Hypoxia_cut_bw1", filter="yes")You will see an error at the end of the execution
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It gives me following error.
ERROR: dependency ‘annotate’ is not available for package ‘genefilter’ * removing ‘/home/eymann/R/x86_64-pc-linux-gnu-library/3.2/genefilter’
The downloaded source packages are in ‘/tmp/RtmplKESiB/downloaded_packages’ Loading required package: edgeR Loading required package: limma Loading required package: ggplot2 Loading required package: gplots
Attaching package: ‘gplots’
The following object is masked from ‘package:stats’:
lowessLoading required package: genefilter 2018-02-06 11:52:21 Starting quality control analysis of Hypoxia_cut_bw1 Error in QC_EdgeR(projectdir = "/home/eymann/Documents/Tools/cbbio/Examples/basic_examples/miRNAs/Known_miRNAs/results/", : could not find function "rowSds" In addition: Warning messages: 1: In install.packages(pkgs = doing, lib = lib, ...) : installation of package ‘XML’ had non-zero exit status 2: In install.packages(pkgs = doing, lib = lib, ...) : installation of package ‘annotate’ had non-zero exit status 3: In install.packages(pkgs = doing, lib = lib, ...) : installation of package ‘genefilter’ had non-zero exit status 4: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : there is no package called ‘genefilter’
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wow, that's new ... What distro (and version) are you using ?
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- attached mRNA_pipeline_error.txt
I am using Ubuntu 16.04 LTS. But this issue seems like solved because installation of genefilter
source("http://bioconductor.org/biocLite.R") biocLite() biocLite("genefilter") library(genefilter)
but now I have another issue while analyzing mRNA data which I attached also.
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Hi, please execute this command using a sudo user:
sudo apt-get -y install vim make gcc openjdk-8-jdk r-base tar bzip2 pkg-config libxml2-dev libcurl4-gnutls-dev
About your "new" error, I'll need again both logs files. Although that error is 99% related with ensemble biomaRt
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- attached miARma_logfile.25502.log
- attached miARma_stat.25502.log
These are 2 log files of mRNA pipeline
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Thanks. So I see that you have successfully finished the differential expression part with edgeR and noiseq ( files TSA_top_bw2_EdgeR_results_Comp.xls and TSA_top_bw2_NOISeq_results_Comp.xls). So for the Functional Analysis we hace to heck again R and Biocondcitr modules.
Could you enter in /home/eymann/Documents/Tools/cbbio/ and execute R?. Then in the R console you need to enter these three commands:
source("./lib/CbBio/RNASeq/R-Scripts/F_Analysis.R") setwd("/home/eymann/Documents/Tools/cbbio/Examples/basic_examples/mRNAs/results/Functional_Analysis_results") F_Analysis(projectdir="/home/eymann/Documents/Tools/cbbio/Examples/basic_examples/mRNAs/results/Functional_Analysis_results",up="/home/eymann/Documents/Tools/cbbio/Examples/basic_examples/mRNAs/results/Functional_Analysis_results/.up_entities_edgeR.txt",down="/home/eymann/Documents/Tools/cbbio/Examples/basic_examples/mRNAs/results/Functional_Analysis_results/.down_entities_edgeR.txt",universe="/home/eymann/Documents/Tools/cbbio/Examples/basic_examples/mRNAs/results/Functional_Analysis_results/.universe_entities_edgeR.txt",organism="human",method="edgeR",seq_id="transcript_id",label="TSA_top_bw2_Comp")This should explain the error properly
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When I right these commands in R it start installing following packages
Bioconductor version 3.2 (BiocInstaller 1.20.3), ?biocLite for help A new version of Bioconductor is available after installing the most recent version of R; see http://bioconductor.org/install BioC_mirror: https://bioconductor.org Using Bioconductor 3.2 (BiocInstaller 1.20.3), R 3.2.3 (2015-12-10). Installing package(s) ‘goseq’, ‘biomaRt’, ‘geneLenDataBase’ also installing the dependencies ‘RCurl’, ‘rtracklayer’, ‘GenomicFeatures’
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and after installing when I tried to do functional analysis it gives the same error
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Did you install the packages that I sent you?:
sudo apt-get -y install vim make gcc openjdk-8-jdk r-base tar bzip2 pkg-config libxml2-dev libcurl4-gnutls-dev -
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Hi Ana, Thanks for using miARma
Before checking your log files, did you install R & bioconductor ? This is needed before using miARma. When installing Biocondfutor, you have also to select the personal library folder (when asked). Did you follow these steps?
Edu