User: amandine.fournier@chu-lyon.fr

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Posts by amandine.fournier@chu-lyon.fr

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GOseq at a specific level ?
... Dear all, I am using GOseq on a list of diffentially expressed genes and I would like to do an analysis at a specific GO level (level 4 for example) instead of the complete GO. Is there a tool in GOseq that already does it ? Or do I have to prepare the file for the gene2cat option by myself ? A so ...
go goseq written 5.1 years ago by amandine.fournier@chu-lyon.fr80 • updated 5.1 years ago by Nadia Davidson270
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Questions about GOseq after DESeq2
... Dear Bioconductor users and developers, I have 2 questions regarding a gene ontology analysis of RNA-Seq data. I first used the DESeq2 package to perform the differential analysis of my data and it resulted in a list of about 500 DEG. Now I would like to perform a gene ontology analysis on this d ...
goseq deseq2 written 5.2 years ago by amandine.fournier@chu-lyon.fr80 • updated 5.2 years ago by Michael Love23k
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Question about ReportingTools used with DESeq2
... Hi, I am currently using the last version of the DESeq2 package to analyse some RNA-Seq data. I would like to use the ReportingTools package to export the results, but I am facing a warning. My code is : > library("DESeq2") > sampleFiles = c("htseqcount_Sample_1.txt","htseqcount_Sample_2.t ...
go bsgenome reportingtools deseq2 written 5.4 years ago by amandine.fournier@chu-lyon.fr80 • updated 5.4 years ago by James W. MacDonald49k
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Releases of DESeq2
... Dear Michael, Simon, Wolfgang and others, I have noticed that new versions of your nice DESeq2 package are released pretty often, which is really great, because it really improves the results. But as a consequence, I wonder when I can "freeze" my analyses. I sometimes have the feeling that there a ...
deseq2 written 5.4 years ago by amandine.fournier@chu-lyon.fr80 • updated 5.4 years ago by Michael Love23k
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Questions about DESeq2 (new version and filtering low counts)
... Dear Mike and others, Thank you Mike for your reply yesterday at my last question about PCA and transformed data. I have two other questions for you today ;-) The first question is about your new version of DESeq2 : - I found about 140 DEG when I used a previous version (v1.0.9) - No ...
deseq2 written 5.5 years ago by amandine.fournier@chu-lyon.fr80 • updated 5.5 years ago by Michael Love23k
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Question about PCA and transformed data in DESeq2
... Dear Michael, Simon, Wolfgang and others, I am a little bit confused about the count data transformations and the Principal Component Analysis in DESeq2. In the last vignette, the example on pages 18-19 shows a PCA plot of the samples, obtained with regularized log transformed data (rld). But in ...
deseq2 written 5.5 years ago by amandine.fournier@chu-lyon.fr80 • updated 5.5 years ago by Michael Love23k
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A few questions about DESeq2 (estimation of dispersion and results table)
... Dear list, I am really interested in using DESeq2 and I have carefully read the vignette, but I am not sure to have all correctly understood. I have a few questions about the dispersion estimated with the estimateDispersions() function : 1. What is the default option used with fitType ? Is it the n ...
deseq deseq2 written 6.0 years ago by amandine.fournier@chu-lyon.fr80 • updated 6.0 years ago by Michael Love23k

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Popular Question 5.1 years ago, created a question with more than 1,000 views. For Questions about GOseq after DESeq2

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