User: Ioannis Vlachos

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40
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Last seen:
5 years, 11 months ago
Joined:
6 years, 7 months ago
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i*@on.gr

Posts by Ioannis Vlachos

<prev • 4 results • page 1 of 1 • next >
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Comment: C: DexSeq extracols option
... Hello, One small tip that I found out the hard way. In DEXSeqHTML the results table [ results <- DEUresultTable(ecs)] is rounded to the third digit prior to padj filtering. Therefore, this might create discrepancies in nrows between the extraCols data.frame and the result table. So the reci ...
written 5.9 years ago by Ioannis Vlachos40
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Comment: C: DexSeq extracols option
... Hello Alejandro and thanks for the prompt response, I am using DEXSeq 1.6, so that was not the problem. The second part of your advice was the solution to my torment. I will elaborate further, just in case anyone faces a similar situation. I was using all the geneIDs present in my ecs object. H ...
written 5.9 years ago by Ioannis Vlachos40
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DexSeq extracols option
... Hello, A (hopefully) simple question. As I saw in ??DEXSeqHTML, there is an option to add attributes in the HTML results (extracols). I downloaded from biomaRt a set aof attributes to test this (gene name, biotype and description), and created a data frame having as a first column the exons of my ...
rnaseq microarray genetics annotation normalization infrastructure cancer probe limma written 5.9 years ago by Ioannis Vlachos40 • updated 5.9 years ago by Alejandro Reyes1.7k
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DESeq and EdgeR log fold differences
... Hello everyone, I thought of conducting a parallel DE analysis with EdgeR and DESeq using a dataset that I have been working on lately. The dataset has two conditions with two biological replicates each. Let's say: Wild Type, Wild Type, Knock Out, Knock Out. It's a smallRNA-Seq dataset, mapped t ...
normalization edger deseq written 6.6 years ago by Ioannis Vlachos40 • updated 6.6 years ago by Gordon Smyth37k

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