Error Could Not Find Function Plotdispests
Contents |
• 12k Guest User • 12k wrote: I have a warning message when I estimate the dipersion parameter. I can't could not find function ggplot2 carry on because of some other error messages in the following steps, could not find function r as I attached below. Thanks in advance -- output of sessionInfo(): sizeFactors (ecs) 7A31.counts 7A32.counts 7A33.counts 46BR1.counts 46BR2.counts 46BR3.counts
R Could Not Find Function User Defined
1.0177858 1.0753635 1.1738656 0.9085247 0.9827212 0.9198726 > ecs<- estimateDispersions ( ecs ) Dispersion estimation. (Progress report: one dot per 100 genes) ...................................................................... ............................................................. Warning messages: 1: In .local(object, ...) : Exons
Error: Could Not Find Function "ddply"
with less than 11 counts will be discarded. For more details read the documentation, parameter minCount 2: In .local(object, ...) : Genes with more than 70 testable exons will be kicked out of the analysis. For more details read the documentation, parameter maxExon > ecs <- fitDispersionFunction(ecs) Error in if (sum(log(coefs/oldcoefs)^2) < 0.005) break : missing value where TRUE/FALSE needed In addition: error: could not find function "opts" Warning messages: 1: In glmgam.fit(mm, disps[good], start = coefs) : Too much damping - convergence tolerance not achievable 2: In log(coefs/oldcoefs) : NaNs produced > head( fData (ecs)$dispBeforeSharing) [1] 0.000000e+00 6.003931e-03 4.852941e-03 0.000000e+00 2.771527e-10 [6] 0.000000e+00 > ecs at dispFitCoefs [1] NA NA > head(fData(ecs)$dispFitted) [1] NA NA NA NA NA NA > plotDispEsts(ecs) Error: could not find function "plotDispEsts" > ecs<-testForDEU(ecs) Error in testForDEU(ecs) : No dispersion values found, call function fitDispersionFunction first. > -- Sent via the guest posting facility at bioconductor.org. ADD COMMENT • link • Not following Follow via messages Follow via email Do not follow modified 2.4 years ago by Alejandro Reyes • 1.3k • written 2.4 years ago by Guest User • 12k 0 2.4 years ago by Alejandro Reyes • 1.3k Germany Alejandro Reyes • 1.3k wrote: Dear Carriero, I think you forgot to copy the output of your sessionInfo()? I think you might be using a very old version of DEXSeq. If so, could you please update at least to the current release version of DEXSeq (1.10.3), try again and write back if it keeps givi
Click here to register now, and join the discussion Community Links Members List Search Forums Show Threads Show Posts Tag Search Advanced Search Go to Page... Similar Threads Thread Thread Starter Forum Replies Last Post ShortRead package
Error In Eval(expr, Envir, Enclos)
bioinfosm Bioinformatics 9 06-01-2014 09:25 AM Using Trinity package aevgup RNA Sequencing 8 02-04-2012 there is no package called ‘rcpp’ 02:15 AM cytochrome Tool/Package t.p.w Bioinformatics 0 01-13-2012 02:04 AM Simulation package in R Jasmine Bioinformatics 0 07-05-2011 08:27 AM a question install ggplot2 about the use of R package-GenomicFeatures masylichu Bioinformatics 5 12-08-2010 05:26 PM Thread Tools 09-30-2011, 10:11 PM #1 elisadouzi Member Location: US Join Date: Mar 2011 Posts: 20 DESeq package(1.5.24) have someone https://support.bioconductor.org/p/59712/ try the new DESeq package(1.5.24) ? I get some error Error: could not find function "plotDispEsts" . Thanks ! lulu elisadouzi View Public Profile Send a private message to elisadouzi Find More Posts by elisadouzi 10-01-2011, 02:02 AM #2 Wolfgang Huber Senior Member Location: Heidelberg, Germany Join Date: Aug 2009 Posts: 108 Lulu, documentation for the DESeq package comes with the package, and you can access it e.g. http://seqanswers.com/forums/showthread.php?t=14465 with typing "help.start()" into R. The documentation is also online, e.g. at http://www.bioconductor.org/packages...tml/DESeq.html The function plotDispEsts is a little helper function defined 'on the fly' when you run the code presented in the vignette. It is not yet defined when you attach DESeq. So, you will need to first run the corresponding part of the code in the vignette (where plotDispEsts is defined) in order to use this function. There may indeed be some benefit in having this function already defined when DESeq is attached, in future versions of the package. Wolfgang __________________ Wolfgang Huber EMBL Wolfgang Huber View Public Profile Send a private message to Wolfgang Huber Visit Wolfgang Huber's homepage! Find More Posts by Wolfgang Huber « Previous Thread | Next Thread » Thread Tools Show Printable Version Email this Page 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 Forum Rules All times are GMT -8. The time now is 06:46 PM. Contact Us - SEQanswers Home - Archive - Top Powered by vBulletin Version 3.8.9Copyright ©2000 - 2016, vBulletin Solutions, Inc. Single Sign On provided by vBSSO
here for a quick overview of the site Help Center Detailed answers to any questions you might have Meta Discuss the workings and policies of this http://stackoverflow.com/questions/7027288/error-could-not-find-function-in-r site About Us Learn more about Stack Overflow the company Business Learn more about hiring developers or posting ads with us Stack Overflow Questions Jobs Documentation Tags Users Badges Ask Question x https://www.biostars.org/p/101220/ Dismiss Join the Stack Overflow Community Stack Overflow is a community of 4.7 million programmers, just like you, helping each other. Join them; it only takes a minute: Sign up Error: could not could not find function … in R up vote 96 down vote favorite 24 I am using R and tried some.function but I got this error message : Error: could not find function `some.function` This question comes up very regularly. When you get the error: could not find function in R, how can you solve it? Thank you in advance for your help. This could not find is meant to be a FAQ question, so please be as complete as possible. The answer is a community answer, so feel free to edit if you think something is missing. This question is approved on meta: http://meta.stackexchange.com/questions/101892/community-wiki-with-common-error-messages-allowed r function error-handling r-faq share|improve this question edited Apr 25 '14 at 9:44 community wiki 11 revs, 6 users 54%Joris Meys 3 Before you vote to close this question, first read this disussion on meta: meta.stackexchange.com/questions/101892/… –Andrie Aug 11 '11 at 14:14 2 If all else fails, try grepping the source code for base R and your installed packages –nullglob Aug 11 '11 at 14:46 3 @nullglob That seems somewhat extreme :-) –Gavin Simpson Aug 11 '11 at 14:51 um, what is wrong . . . –mdsumner Aug 11 '11 at 15:21 I have a relevant question: stackoverflow.com/questions/23357551/…. In this case, ANY R command fails, but q()! Advice will be greatly appreciated! –Aleksandr Blekh Apr 30 '14 at 9:29 add a comment| 8 Answers 8 active oldest votes up vote 63 down vote accepted There are a few things you should check : Did y
faq • rss Community Log In Sign Up Add New Post Question: DEXSeq error while creating ExonCountSet object 0 2.4 years ago by mtiwari • 0 Germany mtiwari • 0 wrote: Hi I am using DEXSeq for my analysis. However, I am facing error while making the ExonCountSet object for further processing. Specifically, on running ecs <- read.HTSeqCounts(sampleTable$countFile, sampleTable, dros_flattened.gff) I get the error: Error in checkAtAssignment("character", "annotationFile", "character") :
‘annotationFile’ is not a slot in class “character”
In addition: Warning message:
'newExonCountSet' is deprecated.
Use 'DEXSeqDataSet' instead.
See help("Deprecated") I prepared the gff file using the dexseq python script, and all other steps alsp as in the DEXSeq vignette. Any suggestions/workarounds are most welcome. Thanks M rna-seq next-gen R • 1.2k views ADD COMMENT • link • Not following Follow via messages Follow via email Do not follow modified 2.4 years ago • written 2.4 years ago by mtiwari • 0 What's the output of sessionInfo()? It's likely that you just need to update all of the packages. ADD REPLY • link written 2.4 years ago by Devon Ryan ♦ 56k The output of sessionInfo() >sessionInfo()
R version 3.1.0 (2014-04-10)
Platform: x86_64-pc-linux-gnu (64-bit) locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=de_DE.UTF-8
[4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=de_DE.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=de_DE.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C attached base packages:
[1] parallel stats graphics grDevice