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Question: Error in reading ballgown object
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gravatar for amy16
8 months ago by
amy160
amy160 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.
This is how I called the ballgown () function:
bg <- ballgown(dataDir="/fast/users/a123456/Ballgown/prr_bulk", samplePattern="B", pData=pheno_data

 

-Thanks

ADD COMMENTlink modified 8 months ago by Alyssa Frazee200 • written 8 months ago by amy160
1
gravatar for Alyssa Frazee
8 months ago by
Alyssa Frazee200
San Francisco, CA, USA
Alyssa Frazee200 wrote:

Hi there -- the error message means that the first column of pData (pheno_data, as you've called it) needs to be in the same order as your list.files() command on your second line (the order of the names of the folders containing the ballgown data). Please rearrange the rows of pData to be in the order B1C, B1T, B2C, B2T, etc (same as list.files -- you can see that the order is currently B1C, B2C, B3C, etc which means the samples won't be labeled correctly). 

ADD COMMENTlink written 8 months ago by Alyssa Frazee200

Hi Alyssa, Thanks for the suggestion. It was helpful. and I was able to get over that error.

ADD REPLYlink written 7 months ago by amy160
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