User: Morris

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Morris0
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Posts by Morris

<prev • 8 results • page 1 of 1 • next >
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rlog in reference level
... Hello everyone, I analyzed RNA-seq data and I noticed that the rlog value of the reference level for some genes are lower then the rest of the samples, how can the Log2FC be negative if the reference level has lower compared to other samples? Thank you ...
deseq2 written 7 days ago by Morris0 • updated 7 days ago by swbarnes2310
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DESeq2 heatmap and rlog transformed values
... Hello everyone, I have a question about values generated with rlog We use the implemented transformation rlog to show HeatMap with the most variable genes among groups/samples, and my question is: are this genes, lets say the top 1000 gene significant in terms of p-value? If I want to see which gen ...
deseq2 written 23 days ago by Morris0 • updated 23 days ago by Michael Love25k
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Comment: C: featureCount and bam
...   Hi b.note, I found the manual thanks.  Let me summarize just to see if I m on the right way...  I have two bam files and I want to perform a differential expression analysis. The first thing to do is to use featureCounts to align and count the reads for all the genes contained in each file.  Is t ...
written 2.2 years ago by Morris0
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featureCount and bam
...   Hi,  I installed Rsubread and now I want to extract raw counts from RNAseq bam files. Could you please give me the command line to use in order to analyse one or more bam files?  thank you    ...
featurecounts written 2.2 years ago by Morris0
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Answer: A: Bam file analysis fro beginner
... Hello,   I was able to reproduce the workflow in the first link, and I have a better idea about the passages needed for the RNAseq analysis. I have a couple of small bam files that I'd like to compare, but I can not find a way to convert this bam file in a package so that can be analyzed in R.  Ho ...
written 2.2 years ago by Morris0
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Answer: A: Bam file analysis fro beginner
... Thank you for the useful links,  I m following the first one, but when I try to import my external data "airway" package I have an error message.   >  dir("bam files") [1] "airway"              "Cell1.bam"           [3] "Cell2.bam"           "RStudio-1.0.143.dmg" > dir("airway") character(0) ...
written 2.3 years ago by Morris0
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BiocLite installation problem
...   Hello everyone,  I am having some problem installing biocLite, the source that I'm using is this one:  source("http://bioconductor.org/biocLite.R") but I get this: Bioconductor version 3.5 (BiocInstaller 1.26.0), ?biocLite for help  Could you please tell me how to figure it out ? Thank you  ...
bioconductor written 2.3 years ago by Morris0 • updated 2.3 years ago by Martin Morgan ♦♦ 23k
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Bam file analysis fro beginner
...     Hi everyone,  I have a couple of bam files from RNAseq that I need to analyze. I'm new to R world and so far I was able to install bioconductor and other packages for the analysis. Could you guys give me links or tutorials including all the passages step by step, from the importation of bam f ...
bioconductor written 2.3 years ago by Morris0

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