Question: Error in reading ballgown object
0
gravatar for amy16
5 months ago by
amy1620
amy1620 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 • 311 views
ADD COMMENTlink modified 5 months ago by WouterDeCoster29k • written 5 months ago by amy1620
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 5 months ago by WouterDeCoster29k

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

ADD REPLYlink written 5 months ago by amy1620
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 5 months ago by WouterDeCoster29k
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 5 months ago • written 5 months ago by amy1620
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