jonathandmoore
commented
1 day ago One thing I thought I would mention if you are new to methylation - most land plants don't have methylation in chloroplast. We use any measured methylation in chloroplast as an estimate of error, since we expect it to be zero
Hope this is helpful.
On Fri, 11 Oct 2024, 17:49 lahyusof, @.***> wrote:
Hello there,
I’m currently analyzing chloroplast methylation of five different rice samples and am just generally scratching my head with filtering. I’ve merged the three replicates into one representative track for each rice I’m analyzing. I’ve tried running ‘Filter by Statistical Test’ for replicate data (i.e. t-test/ANOVA and Logistic Regression) and am not able to run the test at p<0.05 or even 0.1. That leaves me with analyzing unreplicated data and I’m currently unsure of what I should do now and would like to ask for recommendations. Is it better to filter statistics based on continuous data or proportions? Chi-square, Windowed Replicates? Are there other things I should consider during analysis?
I would really appreciate a reply for guidance. I’m so new to SeqMonk and methylation analysis in general that I don’t even know what to start analyzing, what parameters to set (eg window size), when and what data to construct my graphs on and just generally, what is the best way to go about this. Thank you
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lahyusof
Hello there,
I’m currently analyzing chloroplast methylation of five different rice samples and am just generally scratching my head with filtering. I’ve merged the three replicates into one representative track for each rice I’m analyzing. I’ve tried running ‘Filter by Statistical Test’ for replicate data (i.e. t-test/ANOVA and Logistic Regression) and am not able to run the test at p<0.05 or even 0.1. That leaves me with analyzing unreplicated data and I’m currently unsure of what I should do now and would like to ask for recommendations. Is it better to filter statistics based on continuous data or proportions? Chi-square, Windowed Replicates? Are there other things I should consider during analysis?
I would really appreciate a reply for guidance. I’m so new to SeqMonk and methylation analysis in general that I don’t even know what to start analyzing, what parameters to set (eg window size), when and what data to construct my graphs on and just generally, what is the best way to go about this. Thank you