User: Omar Mohamed

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Posts by Omar Mohamed

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Comment: C: Why my normalization failed?
... I figured out something. Only the grey dots are statistically significant. In that case that makes sense for these dots. However, how all the genes are that are very far in both average and fold change are not statistically significant?! ...
written 8 days ago by Omar Mohamed0
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Comment: C: Why my normalization failed?
... It depends on cancer tissue, yes. But both of them are lung cancer, but different tissue type ...
written 8 days ago by Omar Mohamed0
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Comment: C: Why my normalization failed?
... Both of them are cancerous cells. They are expected to be very similar. So, MA plot should be not that disperse and literally in the reverse direction across the x-axis, right? ...
written 8 days ago by Omar Mohamed0
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Why my normalization failed?
... Hi, I am learning DGE. I am using DEseq2. I have obtained data from recount2. This plot comparison between 2 different cancerous tissues. What I was expected that the dispersion is a low mean and convergence as the mean increases. (that's the correct normalization as I have learned so far) Here i ...
R rna-seq written 9 days ago by Omar Mohamed0 • updated 9 days ago by i.sudbery10k
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How to subset SummarizedExperiment object with multiple experiments?
... I have a big SummarizedExperiment object. I want to subset all of the tables based on the information in the colData. I think there should be an efficient way rather than piping filters like: ``` filter <- colData(dat)[id ,which(colData(dat)$parameter) == "cancer" ] cancer <- assays(dat)[,fil ...
R rna-seq written 13 days ago by Omar Mohamed0
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Comment: C: How to access TCGA using recount2 in R?
... 'recount::download_study()' if you haven't loaded recount. For load() it is meant if you have downloaded the .Rdata file manually ...
written 14 days ago by Omar Mohamed0
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Comment: C: How to curate ChIP-seq data, then normalize the depth?
... Thank you for your reply. I have been going throught the tutorials for sometime and now I know the basics of ChIP-seq. The thing is that I now want to apply for a question of interest, and all the tutorial follow a similar approch of getting few ChIP-seq and RNA-seq from the same tissue (and same ...
written 6 weeks ago by Omar Mohamed0
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How to curate ChIP-seq data, then normalize the depth?
... I am an absolute beginner, and I am not sure if this question is legit, so I appreciate any comments. I want to use ChIP-seq data for HeLa cells. I usually see the studies loaded multiple tracks of different histone modification or transcription factors of interest. My idea is that I want to combin ...
chip-seq written 6 weeks ago by Omar Mohamed0

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