Question: Error in file(file, "rt") : invalid 'description' argument
0
gravatar for amy16
5 days ago by
amy1610
amy1610 wrote:

Hi, Please advise me to fix the following error while running the R script using ballgown for DGE analysis.

getwd()
[1] "/fast/users/a123456/prrdata"
pheno_data <- read.csv("pardge_phenotype.csv")
bg_par <- ballgown(dataDir = "prrdata", samplePattern = "sample", pData = pheno_data)
Fri Jan 12 09:58:30 2018
**Fri Jan 12 09:58:30 2018: Reading linking tables
Error in file(file, "rt") : invalid 'description' argument**
pheno_data()
Error in pheno_data() : could not find function "pheno_data"
pheno_data
        ids  treatment            genotype
1  sample01    control     High Resistance
2  sample02    control     High Resistance
3  sample03    control     High Resistance
4  sample04    control Moderate Resistance
5  sample05    control Moderate Resistance
6  sample06    control Moderate Resistance
7  sample07    control         Susceptible
8  sample08    control         Susceptible
9  sample09    control         Susceptible
10 sample10 inoculated     High Resistance
11 sample11 inoculated     High Resistance
12 sample12 inoculated     High Resistance
13 sample13 inoculated Moderate Resistance
14 sample14 inoculated Moderate Resistance
15 sample15 inoculated Moderate Resistance
16 sample16 inoculated         Susceptible
17 sample17 inoculated         Susceptible
18 sample18 inoculate

Thanks

rna-seq ballgown R • 97 views
ADD COMMENTlink modified 5 days ago by Kevin Blighe11k • written 5 days ago by amy1610

Dear Amy,

I don't have a lot of experience with ballgown, but I think you need to run the script from the parent directory "/fast/users/a123456", while your data files must be in prrdata.

ADD REPLYlink written 5 days ago by vinayjrao80

Thanks .... It worked!!!!

ADD REPLYlink written 5 days ago by amy1610
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