DEXSeq error

Hello Folks,

I tried to analysis my RNA seq data using DexSeq which is described in the tutorial "Inferring differential exon usage in RNA-Seq data with the DEXSeq package".

suppressPackageStartupMessages( library( "DEXSeq"))
dxd = DEXSeqDataSetFromHTSeq(
  countFiles,
  sampleData=sampleTable,
  design= ~ sample + exon + condition:exon,
  flattenedfile=flattenedFile )

I got this error when I used the above script

Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec,  : 
  line 270365 did not have 3 elements

This is head for an .txt output of Counting reads:

"A1CF":"001"    1
"A1CF":"002"    0
"A1CF":"003"    1
"A1CF":"004"    2
"A1CF":"005"    2
"A1CF":"006"    0
"A1CF":"007"    1
"A1CF":"008"    1
"A1CF":"009"    1
"A1CF":"010"    1

Best

dexseq deseq2 rna-seq

• 1,967 views • link

written 4.1 years ago by Saeed •

What does line 270365 look like? It looks like there's a single row that's causing the error. Additionally, it might help readability if you formatted your post better using the code chunks.

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written 4.1 years ago by Trivas •

To be honest with you I dont know what is it? but I think it is in read count .txt files. I used .py scripts to make read count using Hiseq with this [workflow] [https://bioc.ism.ac.jp/packages/3.4/bioc/vignettes/DEXSeq/inst/doc/DEXSeq.pdf][1]and I used following scripts in R to start analysis

countFiles = list.files("../star_output/star_hiseq_count/", pattern="b.txt", full.names=TRUE)
basename(countFiles)

flattenedFile = list.files("../count_htseq/", pattern="gff", full.names=TRUE)
basename(flattenedFile)

sampleTable = data.frame(
row.names = c( "68b", "69b", "70b","71b", "72b", "73b" ),
condition = c("knockdown", "knockdown", "knockdown", 
"control", "control", "control" ))

suppressPackageStartupMessages( library( "DEXSeq"))

dxd = DEXSeqDataSetFromHTSeq(
  countFiles,
  sampleData=sampleTable,
  design= ~ sample + exon + condition:exon,
  flattenedfile=flattenedFile )

Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec,  : 
  line 270365 did not have 3 elements

really appreciate your help

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updated 4.1 years ago by Ram

• written 4.1 years ago by Saeed •

Don't add answers unless you're answering the top level question. Use Add Comment or Add Reply instead as appropriate. Also, format your code as code using the 101010 button in the toolbar (see image below). I've fixed this for you this time, but please be careful in the future.

About code formatting:

You can use backticks for inline code (`text` becomes text), or select a chunk of text and use the highlighted button to format it as a code block. If your code has long lines with a single command, break those lines into multiple lines with proper escape sequences so they're easier to read and still run when copy-pasted.
code_formatting

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written 4.1 years ago by Ram

Well noted... Thank you very much for your explanation.

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written 4.0 years ago by Saeed •

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