Question: minfi error in read.metharray
0
gravatar for researcher
6 weeks ago by
researcher0
researcher0 wrote:

I am getting following error related to read.metharray, while running my Script,

Error in read.metharray(basenames = files, extended = extended, verbose = verbose,  : 
  !anyDuplicated(basenames) is not TRUE

FYI, I made my sample sheet on my own by removing the information of some of the samples for which the data was missing. I have double checked that now my meth_idat folder has exactly the same number of samples each with 2 idat files as mentioned in my sample sheet. But still getting this error.

Any help will be highly appreciated.

Thanks

ADD COMMENTlink modified 6 days ago by Gordon Smyth37k • written 6 weeks ago by researcher0
Answer: mini error in read.metharray
1
gravatar for Kasper Daniel Hansen
6 weeks ago by
United States
Kasper Daniel Hansen6.4k wrote:

If you're using read.metharray, the base names argument is a vector which is half the length of the number of files, equal to the number of samples. You need to remove the _Grn and _Red from the file names and remove any duplicates.

read.metharray.exp() is probably an easier to use interface.

ADD COMMENTlink written 6 weeks ago by Kasper Daniel Hansen6.4k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 311 users visited in the last hour