Question: Ballgown object construction error
0
gravatar for spaque57
2.5 years ago by
spaque570
spaque570 wrote:

Hello,

 

I have an error that I can't resolve when I'm creating a ballgown object:

> pheno_data = read.csv("HighLow_phenodata_2.csv", sep=";", header=T)
> bg = ballgown(dataDir = "ballgown", samplePattern = "SNBN", pData=pheno_data)

Thu Jun  1 17:38:29 2017
Thu Jun  1 17:38:29 2017: Reading linking tables
Thu Jun  1 17:38:29 2017: Reading intron data files
Thu Jun  1 17:38:30 2017: Merging intron data
Thu Jun  1 17:38:30 2017: Reading exon data files
Thu Jun  1 17:38:31 2017: Merging exon data
Thu Jun  1 17:38:31 2017: Reading transcript data files
Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec,  : 
  scan() attendait 'a real' et a reçu '.'

 

> traceback()
4: scan(file = file, what = what, sep = sep, quote = quote, dec = dec, 
       nmax = nrows, skip = 0, na.strings = na.strings, quiet = TRUE, 
       fill = fill, strip.white = strip.white, blank.lines.skip = blank.lines.skip, 
       multi.line = FALSE, comment.char = comment.char, allowEscapes = allowEscapes, 
       flush = flush, encoding = encoding, skipNul = skipNul)
3: read.table(file, header = TRUE, sep = "\t", colClasses = cc, 
       quote = "")
2: .readTranscript(f, meas)
1: ballgown(dataDir = "ballgown", samplePattern = "SNBN", pData = pheno_data)

 

 

If anyone has an idea to solve it or know a package to do gene expression analysis like ballgown :/

Thank you !

 

error package ballgown scan • 682 views
ADD COMMENTlink modified 2.4 years ago • written 2.5 years ago by spaque570
Answer: Ballgown object construction error
1
gravatar for spaque57
2.4 years ago by
spaque570
spaque570 wrote:

I fund what was the problem. For those who would have this problem:
- I used a gtf file that I created alone
- it was the source of the problem because of the last column

For a GTF file, the values in the last column must be spaced because the columns are separated by tabs.
When generating a GTF file, I had everything tabbed, that's why the scan problem!

ADD COMMENTlink written 2.4 years ago by spaque570
Answer: C: Ballgown object construction error
0
gravatar for Haiying.Kong
2.5 years ago by
Haiying.Kong110
Germany
Haiying.Kong110 wrote:

If it is csv file, why is sep semicolon?

"HighLow_phenodata_2.csv", sep=";"

ADD COMMENTlink written 2.5 years ago by Haiying.Kong110
Answer: Ballgown object construction error
0
gravatar for spaque57
2.5 years ago by
spaque570
spaque570 wrote:

My excel software put ";" but i try with "," and i also get the error :/

ADD COMMENTlink written 2.5 years ago by spaque570

I never used this function, but i would check transcript data files in the ballgown folder.

probably you can find out how ballgown reads in transcript data, and see if you can read the data in same way.

ADD REPLYlink modified 2.5 years ago • written 2.5 years ago by Haiying.Kong110

Thanks for this advice but a can't find any tips on the ballgown script which could occur this error :/

ADD REPLYlink written 2.4 years ago by spaque570

i am not 100% sure.

but, most likely, scan error means read error.

something in your transcript data is not compatible with the function with which ballgown reads in the data.

ADD REPLYlink modified 2.4 years ago • written 2.4 years ago by Haiying.Kong110

Thank you for your help !

I try with different data and phenotype file, and the code works, so i had a problem with my data.

Now i know what to do ;)

ADD REPLYlink written 2.4 years ago by spaque570
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 203 users visited in the last hour