User: Marie Sémon

gravatar for Marie Sémon
Marie Sémon50
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50
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5 years, 9 months ago
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7 years, 1 month ago
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m**********@ens-lyon.fr

Posts by Marie Sémon

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DESeq2 : when the variable of interest is not a factor
... Dear all, I wish to find genes whose expression profile correlates with a variable of interest, which is quantitative (say, the weight of the individuals). Is it possible/a good practice to use DESeq2 for this? One one hand the vignette clearly describes factors (qualitative) variables, but, on th ...
deseq2 written 5.8 years ago by Marie Sémon50 • updated 5.8 years ago by Jose M Garcia Manteiga310
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Comment: C: How to use DESeq to normalize and estimate variance in a RNAseq timecourse analy
... Hi Wolfgang We wanted first to determine a set of genes for which expression level differs statistically between at least one time point and the controls, because we need to estimate the whole set of genes regulated at some point or the other by the treatment. This is why we compared sequentially C ...
written 7.1 years ago by Marie Sémon50
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Comment: C: How to use DESeq to normalize and estimate variance in a RNAseq timecourse analy
... Dear Simon, >> In our dataset, we tried both procedure and we do see a difference in >> the DESeq output. Maybe, as you said, the estimation of dispersion is >> the same for both procedures, but the normalization step (estimation of >> size Factors ) gives different outputs ...
written 7.1 years ago by Marie Sémon50
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Comment: C: How to use DESeq to normalize and estimate variance in a RNAseq timecourse analy
... Hi Simon, Le 09/05/12 22:12, Simon Anders a écrit : > Hi Marie > >> We are wondering what is the best procedure to prepare this dataset for >> this analysis (steps of normalization + variance estimation): >> 1) is it better to start with normalizing + estimating dispersion o ...
written 7.1 years ago by Marie Sémon50
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How to use DESeq to normalize and estimate variance in a RNAseq timecourse analysis
... Dear all, We are using DESeq to analyse differential expression in a RNAseq timecourse analysis (5 time points after treatment + control). The dataset contains 3 replicates for the control, and single measures for each time point. For each timepoint, we aim to extract differentially expressed genes ...
normalization deseq written 7.1 years ago by Marie Sémon50 • updated 7.1 years ago by Wolfgang Huber13k

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