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Question: Ballgown object construction error
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gravatar for spaque57
5 months 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 !

 

ADD COMMENTlink modified 5 months ago • written 5 months ago by spaque570
1
gravatar for spaque57
5 months 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 5 months ago by spaque570
0
gravatar for Haiying.Kong
5 months ago by
Haiying.Kong90
Germany
Haiying.Kong90 wrote:

If it is csv file, why is sep semicolon?

"HighLow_phenodata_2.csv", sep=";"

ADD COMMENTlink written 5 months ago by Haiying.Kong90
0
gravatar for spaque57
5 months ago by
spaque570
spaque570 wrote:

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

ADD COMMENTlink written 5 months 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 5 months ago • written 5 months ago by Haiying.Kong90

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

ADD REPLYlink written 5 months 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 5 months ago • written 5 months ago by Haiying.Kong90

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 5 months ago by spaque570
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