User: Mahdiar Sadeghi

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MahdiarSadeghi
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Posts by Mahdiar Sadeghi

<prev • 7 results • page 1 of 1 • next >
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Comment: C: ImpulseDE2 - help!
... I have had the same experience, the row.names() should be the same as sample id, and more interestingly it is better to sort the time-points before making ImpulseDE object. ...
written 3 months ago by Mahdiar Sadeghi0
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Comment: C: RNA-Seq time series analysis using ImpulseDE2 software
... Following up this thread: Have you find any answer for your second question? ...
written 3 months ago by Mahdiar Sadeghi0
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Comment: C: cutoff for expressed genes in DESeq2
... Why don't you convert them to TPM and use a global threshold? I noticed that "When you use TPM, the sum of all TPMs in each sample are the same. This makes it easier to compare the proportion of reads that mapped to a gene in each sample.", when reading [this blog post][1]. [1]: https://www.rna ...
written 10 months ago by Mahdiar Sadeghi0
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Comment: C: RNAseq analysis on serial sample
... [ImpulseDE][1] is a good way of analyzing time series samples. It gives you the genes that are going down, up or having a transient response. [1]: https://bioconductor.org/packages/release/bioc/html/ImpulseDE.html ...
written 11 months ago by Mahdiar Sadeghi0
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Comment: C: Histogram plot of padj values
... I was checking the website that you provided. This might be helpful: "**Don’t apply false discovery rate control to these p-values** yet. (Why not? Because some kinds of FDR control are based on the assumption that your p-values near 1 are uniform. If you break this assumption, you’ll get way fewer ...
written 11 months ago by Mahdiar Sadeghi0
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Comment: C: Gene Set Enrichment Analysis with RNA-seq data
... Pre-processing and quality control of the data is necessary because of many reasons. Your results might change if you do it. ...
written 11 months ago by Mahdiar Sadeghi0
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Answer: A: PCA Plot componenets
... Whatever that presents the data better. 3D plots might be confusing depending on your data. In general, 2 component plots are good for presentation and easy to digest. You can add the 3rd component by color scale. ...
written 11 months ago by Mahdiar Sadeghi0

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