User: Endre Sebestyen

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Posts by Endre Sebestyen

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Comment: C: RNA-seq analysis on mouse data with human contamination in controls
... Salmon does not remove the species ambiguous reads, but tries to resolve them and assign to a given transcript, using the combined human/mouse transcriptome. The human ortholog of the KD has 98% sequence identity, based on biomart, so yeah, maybe I should give up. ...
written 6 months ago by Endre Sebestyen60
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Comment: C: RNA-seq analysis on mouse data with human contamination in controls
... OK, maybe I can drop human_read_percent from the model, and see results then. The TPM is between 0 - 0.1 for all 12 samples, both for the mouse gene and the human ortholog. Wondering if I have other problems too... BTW, based on biomart, I have a one 2 one ortholog, with 98% sequence identity betwe ...
written 6 months ago by Endre Sebestyen60
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RNA-seq analysis on mouse data with human contamination in controls
... Hi all, I recently started analysing a mouse RNA-seq dataset, where I had the following data: 6 control samples, all of them contaminated with a human cell line 6 KD samples with no contamination After seeing the "experimental setup" my first thought was to just trash it, take a deep breath, ...
limma rna-seq salmon tximport written 6 months ago by Endre Sebestyen60 • updated 6 months ago by Aaron Lun17k
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RNA-seq analysis without replicates using tximport and DESeq2
... Hi all, I need to reanalyse an RNA-seq experiment with 2 conditions and unfortunately no replicates. I probably don't have big changes in expression, 100-200 genes with logFC max 2-3. I'm planning to do the the following: Salmon/Kallisto with a recent RefSeq collection to estimate read counts. ...
rnaseq deseq2 tximport written 12 months ago by Endre Sebestyen60 • updated 12 months ago by Michael Love14k
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time course design matrix
... Hi! I'd welcome some help on creating a design matrix for a time-course experiment. I have 7 time points (0,3,6,9,12,24,27 hours) with three technical replicates at each time point. Cy3 is the untreated, Cy5 is the treated sample on each chip. There is an example in the limma user guide for time c ...
limma written 9.5 years ago by Endre Sebestyen60
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Answer: A: basic limma questions
... Dear Gordon, Thanks for the answers. I have one final question. It is true that the Data-Ctrl contrast is the same in both cases, but it makes a difference if my gene is 10x up or 0.1x downregulated compared to the untreated sample. So either I have to change R and G, or use a design <- c(-1,-1 ...
written 9.6 years ago by Endre Sebestyen60
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Answer: A: basic limma questions
... Thanks for your answer. A little more details : I had a control and a treatment, with 3 technical replicates and no dye-swaps. Cy3 was the treated, Cy5 the untreated. The ArrayVision result file looks like this : Ctrl Ctrl Ctrl Data Data Data Spot la ...
written 9.6 years ago by Endre Sebestyen60
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Answer: A: basic limma questions
... Again : Hi! I'm a beginner in limma and bioconductor, and I'd like to ask a few basic questions. I wrote the following script : library(limma) targets <- readTargets("Targets1.txt") RG <- read.maimages(targets$FileName, columns=list(R="CtrlVol", G="DataVol", Rb="CtrlBg", Gb="DataBg"), anno ...
written 9.6 years ago by Endre Sebestyen60
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basic limma questions
... Hi! I'm a beginner in limma and bioconductor, and I'd like to ask a few basic questions. I wrote the following script : library(limma) targets <- readTargets("Targets1.txt") RG <- read.maimages(targets$FileName, columns=list(R="CtrlVol", G="DataVol", Rb="CtrlBg", Gb="DataBg"), annotation=c( ...
limma written 9.7 years ago by Endre Sebestyen60

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