User: sirintra
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Posts by sirintra
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... 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 2.6 years ago by
sirintra • 0
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... 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 ...
written 2.6 years ago by
sirintra • 0
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... 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 ...
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... 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 4.0 years ago by
sirintra • 0
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... 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 4.0 years ago by
sirintra • 0
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... 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 ...
written 4.0 years ago by
sirintra • 0
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For edgeR time series analysis with no replicates
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