User: pokharel.kisun

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Posts by pokharel.kisun

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Comment: C: differential expression analysis using deseq2
... Thanks! I slightly modified to include more than one groups. dds_fFS_TX <- dds[ , dds$group %in% c("FS.F" ,"TX.F")] ...
written 3.8 years ago by pokharel.kisun0
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Comment: C: differential expression analysis using deseq2
... Hi Mike, finally I have been able to understand those results. Would it be possible to make a PCA plot for the subsets such as FS.F and TX.F? I am particularly interested to see the clustering for contrasts with many DE genes. ...
written 3.8 years ago by pokharel.kisun0
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Comment: C: differential expression analysis using deseq2
... Hello Mike, I got the results but unable to figure out what the results are really trying to tell. The first comparision shows that there are very few differences between breeds due to diet differences and also the within-breed comparision in FS shows there is not diet effect in FS. However, FS.F vs ...
written 3.9 years ago by pokharel.kisun0
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Comment: C: differential expression analysis using deseq2
... Thanks a lot Mike. I am still confused with the later design... I found around 200 genes that are differentially expressed between FS and TX, can't there be some genes which were differentially expressed due to diet? One of the breed is responsive to diet while the other is not. I have 10 samples (4 ...
written 3.9 years ago by pokharel.kisun0
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differential expression analysis using deseq2
... Hi, I am doing DE analysis on three breed groups (FS, TX, F1) with two diet conditions (C, F, where C is the normal diet and F is the additional diet). I want to find DE genes between breeds (FS vs TX, FS vs F1 and TX vs F1) both with diet effect and without diet effect. In addition, I want to find ...
deseq2 multiple factor design written 3.9 years ago by pokharel.kisun0 • updated 3.9 years ago by Michael Love26k

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