User: sirintra

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sirintra0
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Posts by sirintra

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Answer: A: Using edgeR for small shRNA-seq screen analysis
... Dear Matthew, Thank you for your reply. It was really helpful. If you don't mind, I have a few more questions, just to make sure that I understand your suggestions correctly. - I had a read through section 4 again, and noticed that TMM was applied before model fitting in this example. So I was won ...
written 23 days ago by sirintra0
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Using edgeR for small shRNA-seq screen analysis
... Hi, I have a very small shRNA-seq screen dataset that contains only 36 shRNAs (targeting a total of 17 genes) with one shRNA being a control (i.e. no change in its representation is expected over time). Most of the other shRNAs targeting genes that are thought to be essential for cell survival. It ...
edger shrna written 25 days ago by sirintra0
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Invalid vertex id while running R_igraph_spinglass_my_community on FEM package
... Hi, I have used bioconductor package FEM on my 450k methylation and RNAseq data. I followed the instruction described in the vignette. I can manage to run DoEpiMod and DoExpMod functions on the methylation and RNAseq datasets successfully independently. However, when I tried to run DoFEMbi on the s ...
igraph fem written 16 months ago by sirintra0 • updated 16 months ago by andrew0
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Answer: A: edgeR time series analysis with no replicates
... Dear Aaron, Thank you very much for the example code and excellent explanation. I have followed your suggestion and got a lot more genes with significant test results than my previous approach. There are a few more things regarding the results that I’d like to clarify and would appreciate your thou ...
written 18 months ago by sirintra0
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Answer: A: edgeR time series analysis with no replicates
... I have in total of 8 samples for 4 timepoints. So two samples (one control and one treatment) for each time point. Let me know if you need more information. Thanks a lot. ...
written 18 months ago by sirintra0
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edgeR time series analysis with no replicates
... Hi, I have RNAseq data from an shRNA knockdown screening experiment and I 'm trying to perform differential test using EdgeR. What we are interesting in is the difference between control and treatment (Dox) at the last time point compared to the first time point. So my design matrix is as follow an ...
edger written 18 months ago by sirintra0

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