Question: Error in reading ballgown object
0
gravatar for amy16
2.5 years ago by
amy1640
amy1640 wrote:

Hi, Can someone please advise me on this error?

> pheno_data
  ids  treatment    genotype
1 B1C    control   Resistant
2 B2C    control Susceptible
3 B3C    control   Resistant
4 B4C    control Susceptible
5 B1T inoculated   Resistant
6 B2T inoculated Susceptible
7 B3T inoculated   Resistant
8 B4T inoculated Susceptible
> list.files()
[1] "B1C" "B1T" "B2C" "B2T" "B3C" "B3T" "B4C" "B4T"
Error in ballgown(dataDir = "/fast/users/a123456/Ballgown/prr_bulk",  :
  first column of pData does not match the names of the folders containing the ballgown data.
In addition: Warning message:
In ballgown(dataDir = "/fast/users/a123456/Ballgown/prr_bulk",  :
  Rows of pData did not seem to be in the same order as the columns of the expression data.

-Thanks

rna-seq ballgown R • 1.1k views
ADD COMMENTlink modified 2.5 years ago by WouterDeCoster44k • written 2.5 years ago by amy1640
1

I added code markup to your post for increased readability. You can do this by selecting the text and clicking the 101010 button. When you compose or edit a post that button is in your toolbar, see image below:

101010 Button

ADD REPLYlink written 2.5 years ago by WouterDeCoster44k

ok. Thanks... Any leads into fixing the error?

ADD REPLYlink written 2.5 years ago by amy1640
1

first column of pData does not match the names of the folders containing the ballgown data

This looks pretty clear, or at least suggest you that the first column of pData (pheno_data?) should match the names of the folders containing the ballgown data.

Your command above is also incomplete: you never show us how you call the ballgown() function.

ADD REPLYlink written 2.5 years ago by WouterDeCoster44k
Sorry, I thought I had it earlier.
This is how I called the ballgown () function:
 bg <- ballgown(dataDir="/fast/users/a123456/Ballgown/prr_bulk", samplePattern="B", pData=pheno_data)
ADD REPLYlink modified 2.5 years ago • written 2.5 years ago by amy1640
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