Need help to understand a problem in a R script

Question

[psschlogl]

Hi guys I am really sorry to bother you to help me on this! I am following a tutorial that I am almost finishing but I got to understand what its going on. I have a csv like this:

$>cat UHR_vs_HBR.csv
"ids","type","path"
"UHR_Rep1","UHR"," /media/paulo/44691167-b916-42ad-87f0-b215c6ef2e6c/paulo/bioinfo/griffithlab/RNAseq_Bioinformatics/RNA_DIR/expression/stringtie/ref_only/UHR_Rep1"
"UHR_Rep2","UHR"," /media/paulo/44691167-b916-42ad-87f0-b215c6ef2e6c/paulo/bioinfo/griffithlab/RNAseq_Bioinformatics/RNA_DIR/expression/stringtie/ref_only/UHR_Rep2"
"UHR_Rep3","UHR"," /media/paulo/44691167-b916-42ad-87f0-b215c6ef2e6c/paulo/bioinfo/griffithlab/RNAseq_Bioinformatics/RNA_DIR/expression/stringtie/ref_only/UHR_Rep3"
"HBR_Rep1","HBR"," /media/paulo/44691167-b916-42ad-87f0-b215c6ef2e6c/paulo/bioinfo/griffithlab/RNAseq_Bioinformatics/RNA_DIR/expression/stringtie/ref_only/HBR_Rep1"
"HBR_Rep2","HBR"," /media/paulo/44691167-b916-42ad-87f0-b215c6ef2e6c/paulo/bioinfo/griffithlab/RNAseq_Bioinformatics/RNA_DIR/expression/stringtie/ref_only/HBR_Rep2"
"HBR_Rep3","HBR"," /media/paulo/44691167-b916-42ad-87f0-b215c6ef2e6c/paulo/bioinfo/griffithlab/RNAseq_Bioinformatics/RNA_DIR/expression/stringtie/ref_only/HBR_Rep3"

This csv has the fullpath to the dir(HBR and UHR samples) where are located each of the samples files :
e2t.ctab
e_data.ctab
gene_abundances.tsv
i2t.ctab
i_data.ctab
t_data.ctab
transcripts.gtf

The R script is this one: enter link description here

But at the start i got this error:

    Error in ballgown(samples = as.vector(pheno_data$path), pData = pheno_data) : 
  Something is wrong: are you missing .ctab files? Do extra files/folders (other than tablemaker output folders) match your samples/dataDir/samplePattern argument(s)?

I know that my paths are very weird but I forgot to adjust my Ubuntu installation 8) so... I know that ballgown is complaining about reading the folders and the files in them.

Do you see something I didn't? PS- any other code works with these ugly full paths.

Thank you all! Paulo

---

Update

Hey Guys I tried to clean the space typo, put some others ' " ' that were missing, but still complaining. 8(

    Error in ballgown(samples = as.vector(pheno_data$path), pData = pheno_data) : 
  must provide either "samples" or both "dataDir" and "samplePattern"

I will try to make that file again.
I will let you know.
Thanks to all!

UPDATE
I change the samples to a dir ballgown and make the file with paths again and its working!
Thanks to all!
Paulo

[Ram]

You seem to be doing everything right. This is odd. Can you paste the output of:

tree /media/paulo/44691167-b916-42ad-87f0-b215c6ef2e6c/paulo/bioinfo/griffithlab/RNAseq_Bioinformatics/RNA_DIR/expression/stringtie/ref_only/

[psschlogl]

├── UHR_Rep1
│   ├── e2t.ctab
│   ├── e_data.ctab
│   ├── gene_abundances.tsv
│   ├── i2t.ctab
│   ├── i_data.ctab
│   ├── t_data.ctab
│   └── transcripts.gtf
├── UHR_Rep2
│   ├── e2t.ctab
│   ├── e_data.ctab
│   ├── gene_abundances.tsv
│   ├── i2t.ctab
│   ├── i_data.ctab
│   ├── t_data.ctab
│   └── transcripts.gtf
├── UHR_Rep3
│   ├── e2t.ctab
│   ├── e_data.ctab
│   ├── gene_abundances.tsv
│   ├── i2t.ctab
│   ├── i_data.ctab
│   ├── t_data.ctab
│   └── transcripts.gtf
└── UHR_vs_HBR.csv

Its looks like the kind of tree tha ballgown uses:

extdata/
    sample01/
        e2t.ctab
        e_data.ctab
        i2t.ctab
        i_data.ctab
        t_data.ctab
    sample02/
        e2t.ctab
        e_data.ctab
        i2t.ctab
        i_data.ctab
        t_data.ctab
    ...
    sample20/
        e2t.ctab
        e_data.ctab
        i2t.ctab
        i_data.ctab
        t_data.ctab

But I don't know why it doesn't head my data 8(

[Ram]

Yeah, you seem to be doing things the right way. Maybe check permissions on the files? If that doesn't help, maybe someone else can help you out. Sorry!

[zx8754]

If you have more info, please update "edit" your post, use answers box for solutions only.

Answer 1

[Philipp Bayer]

Could it be this:

 "UHR_Rep1","UHR"," /media/paulo/44691167-b916-42ad-87f0-b215c6ef2e6c/paulo/bioinfo/griffithlab/RNAseq_Bioinformatics/RNA_DIR/expression/stringtie/ref_only/UHR_Rep1"

There's an extra space before '/media/' which maaaybe confuses ballgown

[zx8754]

This might be the issue, compare the outputs of:

# no leading space, list all file in current directory
list.files("./")

# [typo?] with leading space
list.files(" ./")

@PhilippBayer, maybe move to answer?

[Philipp Bayer]

Good idea, moved, thanks for that :)