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ANOSIM in R Vegan package
Hi,
I want to check groupings in R using the ANOSIM function which is available through Vegan package. I have used EdgeR to normalize my data and produce an MDSplot based on co-efficient of variations between libraries.
I have downloaded all the need packages. Has anyone ever had any experience with this piece of software and if so,could you kindly provide me with an example command input?
I ask the above as I am novice to R and I am going to be learning this as part of my PhD through-out the next year. My matrix has 3 conditions over 3 days (1 rep for each of the 9 above-I know it's not ideal).
Lets call them A1,A2,A3
B1,B2,B3
C1,C2,C3
Each condition above is a column header, rows are the sequence expression values.
The question is: how do I group them and what permutation value do people go for, what would this be based on for RNA-Seq work? Also which distance metric would pose best for RNA Seq data?
Many thanks.
I want to check groupings in R using the ANOSIM function which is available through Vegan package. I have used EdgeR to normalize my data and produce an MDSplot based on co-efficient of variations between libraries.
I have downloaded all the need packages. Has anyone ever had any experience with this piece of software and if so,could you kindly provide me with an example command input?
I ask the above as I am novice to R and I am going to be learning this as part of my PhD through-out the next year. My matrix has 3 conditions over 3 days (1 rep for each of the 9 above-I know it's not ideal).
Lets call them A1,A2,A3
B1,B2,B3
C1,C2,C3
Each condition above is a column header, rows are the sequence expression values.
The question is: how do I group them and what permutation value do people go for, what would this be based on for RNA-Seq work? Also which distance metric would pose best for RNA Seq data?
Many thanks.