R Read.table Error In Scan
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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 site About Us Learn more read.table eof within quoted string about Stack Overflow the company Business Learn more about hiring developers or posting ads error in read.table more columns than column names with us Stack Overflow Questions Jobs Documentation Tags Users Badges Ask Question x Dismiss Join the Stack Overflow Community Stack Overflow error in read.table duplicate 'row.names' are not allowed is a community of 6.2 million programmers, just like you, helping each other. Join them; it only takes a minute: Sign up Confusing error in R: Error in scan(file, what, nmax, sep, dec, quote,
In Scan(file = File, What = What, Sep = Sep, Quote = Quote, Dec = Dec, : Eof Within Quoted String
skip, nlines, na.strings, : line 1 did not have 42 elements) [duplicate] up vote 19 down vote favorite 10 This question already has an answer here: Error in reading in data set in R 5 answers I am new to R. I am trying to read in a "CSV" file that is space-space delimited. The file does not have headers. It looks like this Element1 Element2 Element5 Element6 Element7 I r fill=true am trying to read it in like this: > mydata <- read.table("/PathTo/file.csv") Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, : line 1 did not have 14 elements Why does it expect 14 elements in the first row? How do I import this file? r share|improve this question asked Oct 18 '13 at 16:55 bernie2436 3,9551866145 marked as duplicate by Frank, rcs, liyakat, Jilber, Dour High Arch Oct 19 '13 at 16:28 This question has been asked before and already has an answer. If those answers do not fully address your question, please ask a new question. @SimonO101 if you put that as an answer I will accept –bernie2436 Oct 18 '13 at 17:19 Your data is not in the table format, why use read.table? –Fernando Oct 18 '13 at 17:20 add a comment| 2 Answers 2 active oldest votes up vote 39 down vote accepted read.table wants to return a data.frame, which must have an element in each column. Therefore R expects each row to have the same number of elements and it doesn't fill in empty spaces by default. Try read.table("/PathTo/file.csv" , fill = TRUE ) to fill in the blanks. e.g. read.table( text= "Element1 Element2 Element
using R and the shell: a casestudy Once in a while, you embark on what looks like a simple computational procedure only to encounter frustration very early on. "I can't even read my file into R!" you cry. r read table fill Step back, take a deep breath and take note of what the software
Read Table Fill True
is trying to tell you. Most times, you've just missed something very straightforward. Here's an example. Update: this post
Scan() Expected 'a Real', Got
is not about how best to perform the task; it's about how to cope with frustration. Please stop sending me your solutions :-) Recently, I was trying to retrieve some data describing http://stackoverflow.com/questions/19455070/confusing-error-in-r-error-in-scanfile-what-nmax-sep-dec-quote-skip-nli characteristics of microbial genomes from the NCBI FTP site. The file, lproks_0.txt (direct link), looked like a regular tab-delimited file with a couple of header lines: head lproks_0.txt ## Microbial Organism Information Page ## Columns: "RefSeq project ID" "Project ID" "Taxonomy ID" "Organism Name" "Super Kingdom" "Group" "Sequence Status" "Genome Size" "GC Content" "Gram Stain" "Shape" "Arrangment" "Endospores" "Motility" "Salinity" "Oxygen Req" "Habitat" https://nsaunders.wordpress.com/2011/04/08/fixing-aberrant-files-using-r-and-the-shell/ "Temp. range" "Optimal temp." "Pathogenic in" "Disease" "Genbank accessions" "Refseq accessions" 49725 30807 551115 'Nostoc azollae' 0708 Bacteria Cyanobacteria complete 5.532 38.3 Filaments Filaments Yes Aerobic Multiple Mesophilic - CP002059,CP002060,CP002061 - 55729 33011 592010 Abiotrophia defectiva ATCC 49176 Bacteria Firmicutes assembly 3.4774 37.1 + Cocci NoNo Facultative - ACIN00000000 - Sharp eyes will notice a problem right there, on the first line of data. Less sharp-eyed users like me will open an R console to read the file, expecting no issues: genomes <- read.table("lproks_0.txt", header = F, skip = 2, stringsAsFactors = F, sep = "\t") Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, : line 376 did not have 23 elements
"I can't even read my file into R!" My first mistake: reach for the tool that I know best, not the tool which is appropriate. In this case, my instinct was to count the fields in a line using awk. Since we skipped the first 2 lines in R, we want to examine line 378 in the original file: awk '{FS="\t"; print NF}' lproks_0.txt | head -n 378 | nl | tail -n1faq • rss Community Log In Sign Up Add New Post Question: R: Error In Scan ... Line 7 Did Not Have 3 Elements 0 2.9 years ago by silkeverhelle • 10 silkeverhelle • 10 wrote: Hi, i'm trying to normalize https://www.biostars.org/p/87836/ my data but i get the following error: celfiles <- read.affy(covdesc="silke.txt", path="data") Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, : line 7 did not have 3 elements my txt file seems to be normal. I already searched for answers, but i don't know where i made a mistake Thanks!! R affymetrix • 6.6k views ADD COMMENT • link • Not following Follow via messages Follow via email Do not follow modified 2.9 years error in ago • written 2.9 years ago by silkeverhelle • 10 3 Hi Silke, please follow the guidelines for submitting an error in R: post the output of traceback() post a reproducible example (silke.txt, it is most likely the source of error) post the output of sessionInfo() Thanx! ADD REPLY • link modified 2.9 years ago • written 2.9 years ago by Michael Dondrup ♦ 39k 2 This error means what it says; the text file is not (tab) eof within quoted delimited in the way that you think. Most often this happens when lines contain comment characters (#) or single quotes. Read the help page for read.table() for ways to deal with this. ADD REPLY • link written 2.9 years ago by Neilfws ♦ 46k 0 2.9 years ago by silkeverhelle • 10 silkeverhelle • 10 wrote: I found a solution. Thanks for your reactions ADD COMMENT • link written 2.9 years ago by silkeverhelle • 10 3 Please, post your solution. ADD REPLY • link written 2.9 years ago by zx8754 ♦ 3.3k 1 Yes, please do. The point of this site is to provide answers for everyone. This post is not an answer. ADD REPLY • link modified 2.9 years ago • written 2.9 years ago by Neilfws ♦ 46k Please log in to add an answer. Similar posts • Search » Puzzling Error Message While Working Through A Bioconductor Tutorial On Microarrays I tried recently somme tutorial on microarray data analysis, using either the following link: htt... Question: Getgeo Error - line 1 did not have 6 elements It's my first Question. Hope someone can help me to solve that problem. Why I can download GEO ... Follow-Up Question: How To Import Annotation File Into R? As a follow-up question to Where to find annotation file for Agilent microarray? : Does anyone h... Biomart Refseq Data Problem Hello,