User: emb13

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emb130
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Posts by emb13

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How to align loci to in silico digested fragments
... Hi all, I am trying to figure out how to align loci to in silico digested fragments. I would like to map ~50,000 loci from an RRBS experiment back to the fragments which resulted from the restriction enzyme digestion, but I am not sure how to do it. My goal is to determine if the loci are localized ...
in silico digestion written 6 months ago by emb130 • updated 6 months ago by Julie Zhu4.0k
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Comment: C: EdgeR -- differentially expressed genes across a continuous variable
... Thank you for your help! ...
written 8 months ago by emb130
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EdgeR -- differentially expressed genes across a continuous variable
... Hi all, I am working on an RNAseq experiment where we have three experimental doses and a control. I have completed the analysis using the dose as a group assignment, but I am curious about genes which have a linear relationship across the gradient of doses. My initial approach was to identify DEGs ...
regression edger continuous written 8 months ago by emb130 • updated 8 months ago by James W. MacDonald51k
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Comment: C: EdgeR RNAseq -- best way to deal with random effects
... Thank you again for the feedback, Aaron! ...
written 10 months ago by emb130
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Comment: C: EdgeR RNAseq -- best way to deal with random effects
... Hi Aaron, Thank you so much for your reply. It is correct that dose is completely nested in mesocosm (see my comment to Gordon above). Because of this I have decided to try the third option as this best represents the interaction between group and mesocosm which is apparent in my MDS plot. Is setti ...
written 10 months ago by emb130
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Comment: C: EdgeR RNAseq -- best way to deal with random effects
... Hi Gordon, Thank you for your reply. All mesocosms are at the same physical site, but the site is broken down into fenced in "pads" which contain the mesocosms (which are individual cattle tanks). Thus, the S1 mesocosms (S1h, S1m, S1l, S1c) are within one fenced pad. The pads are very close to one ...
written 10 months ago by emb130
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EdgeR RNAseq -- best way to deal with random effects
... Hello, I am working on an RNAseq project in EdgeR and I have a random effect variable that I am not sure how to best deal with since EdgeR doesn't use mixed models. I have three main questions: 1) how have people dealt with random effects in EdgeR, or do you use different programs to accomplish thi ...
rnaseq edger written 11 months ago by emb130 • updated 11 months ago by Aaron Lun25k

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