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News: Bioconductor teaching week
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Job: Lecturer in Statistics - School of Mathematics and Statistics - University of St Andrews
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Job: Bioconductor Community Manager
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Job: Research software engineer at the de Duve Institute, UCLouvain (Brussels, Belgium)
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EdgeR: Explaning dispersion types to newbies
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News: New Master of Science in Quantitative and Computational Biology at University of Trento, Italy
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News: Bioconductor-related papers -- special F1000Research collection for Bioc2016
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updated 7.5 years ago by ▴ 10 • written 7.5 years ago by 13k
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Comment: Deseq2 calculated log2foldchange not consistent with RPM in IP-small RNA-seq by Shihui • 0
It makes sense that DeSeq2 normalized FPMs are more accurate. Thank you for the information!
Answer: DiffBind - how to prep the sample matrix when multiple bam files are used by MAC by James W. MacDonald 63k
If you essentially combined multiple BAM files in the MACS call, you could then just combine them using `samtools cat`, in which case you o…
Comment: Deseq2 calculated log2foldchange not consistent with RPM in IP-small RNA-seq by Michael Love 40k
I can rephrase your question as: Why is number of reads not the superior estimate for the scaling factor (the "m" in rpm). There are som…
Comment: Deseq2 calculated log2foldchange not consistent with RPM in IP-small RNA-seq by Shihui • 0
Hi Michael, Yes I manually calculated the RPMs by dividing each genes RPM to the library read depth. I didn't do any other normalization …
Comment: shinyMethyl - saving the file by dorota.komar • 0
I tried printing the page as pdf, unfortunately I get the same problem. I guess for now, I will need to save the graphs separately :) Than…
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Answer: Deseq2 calculated log2foldchange not consistent with RPM in IP-small RNA-seq
Comment: Deseq2 calculated log2foldchange not consistent with RPM in IP-small RNA-seq
Batch correction and Deseq2
A: Read counts between QSEA and MEDIPs
ComBat_seq function in sva package does not return a matrix
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