User: Hugo Varet

gravatar for Hugo Varet
Hugo Varet80
Reputation:
80
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Trusted
Location:
France
Last seen:
1 year, 7 months ago
Joined:
5 years, 5 months ago
Email:
h*********@pasteur.fr

Posts by Hugo Varet

<prev • 8 results • page 1 of 1 • next >
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Answer: A: DESeq2 size factors estimation after RSEM quantification
... Dear Mike, thanks for you answer and your advices. I added a check in my script to deal with that and continue the analysis. I am not very familiar with RSEM, but I think the difficulty comes from the "effective_length" which can be set to zero for some samples and positive for others, depending o ...
written 3.0 years ago by Hugo Varet80
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DESeq2 size factors estimation after RSEM quantification
... Dear Mike Love, I just upgraded DESeq2 to get the last version (1.12.0) and I have a problem when using the estimateSizeFactors() function on a DESeqDataSet object built from RSEM outputs (with the help of tximport). The problem is that infinite values are generated because of the use of the log() ...
deseq2 estimatesizefactors tximport rsem written 3.0 years ago by Hugo Varet80
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Interaction categorical/continuous variable DESeq2
... Dear list, dear Mike Love, I am using DESeq2 to model counts from an unusual type of experiment and I have a question about the strategy I employed. The experiment consisted in sequencing 33 samples for which we have the following information: - group (16 samples from group A and 17 from group B) ...
sequencing deseq2 written 4.7 years ago by Hugo Varet80 • updated 4.7 years ago by Wolfgang Huber13k
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Comment: C: DESeq2 error: inv(): matrix appears to be singular
... Hi Mike, thank you for having fixed the error so quickly ! I've just tried version 1.3.48, it works without any error on my data set. Best regards, Hugo Hugo Varet Plate-Forme Transcriptome et Epig?nome Institut Pasteur M?l. : hugo.varet at pasteur.fr T?l. : 01-40-61-35-13 Le 11/03/2014 23:02, ...
written 5.2 years ago by Hugo Varet80
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Comment: C: DESeq2 error: inv(): matrix appears to be singular
... Sure, here it is : R version 3.0.2 (2013-09-25) Platform: x86_64-w64-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=French_France.1252 LC_CTYPE=French_France.1252 LC_MONETARY=French_France.1252 LC_NUMERIC=C [5] LC_TIME=French_France.1252 attached base packages: [1] parallel stats graphics grD ...
written 5.2 years ago by Hugo Varet80
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DESeq2 error: inv(): matrix appears to be singular
... Dear Mike Love and list members, I'm running DESeq2 with a design containing two covariates: the first is dichotomous while the second is continuous. Here is the data.frame I put in colData(dds): sample dicho conti 1 0 4.577032 2 0 4.462997 ...
deseq2 written 5.2 years ago by Hugo Varet80 • updated 5.2 years ago by Michael Love23k
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Comment: C: Multiple contrasts in DESeq2
... Thank you Mike for having answered very quickly! Best, Hugo Le 23/12/2013 14:45, Michael Love a écrit : > hi Hugo, > > We are not planning at the moment to have results() generate multiple > contrasts, but I will keep it in mind. > > best, > > Mike > > > On Mon, ...
written 5.4 years ago by Hugo Varet80
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Multiple contrasts in DESeq2
... Dear Michael Love and list members, I'm used to analyze RNA-seq data with your nice DESeq2 package (1.2.0) and I sometimes have to test complex null hypotheses using contrasts. For one of my project, I would like using multiple contrasts, i.e. testing for example (H0: beta1-beta2 = beta3-beta4 = 0) ...
deseq2 written 5.4 years ago by Hugo Varet80 • updated 5.4 years ago by Michael Love23k

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Popular Question 4.5 years ago, created a question with more than 1,000 views. For Interaction categorical/continuous variable DESeq2

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