User: AurelieMLB

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AurelieMLB40
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United Kingdom
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4 years, 1 month ago
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Posts by AurelieMLB

<prev • 13 results • page 1 of 2 • next >
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Answer: A: Design formula and Design matrix in DESeq
... Hello, For those like me who needs to familiarise themselves with what formulas in R means, I found those links: - http://stackoverflow.com/questions/13366755/what-does-the-r-formula-y1-mean - http://cran.r-project.org/doc/manuals/R-intro.html#Formulae-for-statistical-models I found this helpful ...
written 4.2 years ago by AurelieMLB40
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Comment: C: Design formula and Design matrix in DESeq
... This is very helpful. Thank you very much for your time.  ...
written 4.2 years ago by AurelieMLB40
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Comment: C: Design formula and Design matrix in DESeq
... Many thanks for your answer. I think you are touching the core of my question here. I did read your paper and the vignettes. I see which paragraph you are talking about. But for me both formulas, ~group and ~time*treatment (and the associated contrasts I am doing) seem to take the interactions into ...
written 4.2 years ago by AurelieMLB40
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Comment: C: Design formula and Design matrix in DESeq
... Hello, Following what I understood from the example your were pointing at, I tried to group my time and treatment in a single factor "group". e.g.: sample  treatment time         group s1 treatment1 1 treatment1.1 s2 treatment2 1 treatment2.1 s3 control 1 control.1 ... (in triplicate and for dif ...
written 4.2 years ago by AurelieMLB40
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Comment: C: Design formula and Design matrix in DESeq
... Thank you very much! ...
written 4.2 years ago by AurelieMLB40
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Comment: C: Design formula and Design matrix in DESeq
... Thanks a lot for this! I am trying both DESeq2 and Limma actually to see if I get similar results. May I ask you how/where you learnt about formulas and designs? Is there something I can do to get a better understanding and be able to understand this by myself rather than having to ask questions on ...
written 4.2 years ago by AurelieMLB40
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Comment: C: DESeq2 with 2 factors: problem to fit the negative binomial and weird p-value di
... Thank you very much ! This is helpful! ...
written 4.2 years ago by AurelieMLB40
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Design formula and Design matrix in DESeq
... Hello, I am new to RNAseq, new to DESeq2 and new to writing design formulas/matrix (not a statistician)... I am trying to understand the meaning of the different examples I find on the internet and so far I am far from a clear understanding. Could someone help please? Is there a documentation for ...
rnaseq limma deseq2 formula written 4.2 years ago by AurelieMLB40
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Comment: C: DESeq2 with 2 factors: problem to fit the negative binomial and weird p-value di
... May I follow up with a complementary question please? The treatments are expected to induce big changes in the samples. So I am expecting to see quite a lot of genes differentially expressed at T24. My understanding is that DESeq2 assumes that the expression of most of genes do not change... Should ...
written 4.2 years ago by AurelieMLB40
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Answer: A: DESeq2 normalisation: is the size of the gene taken into account?
... Thank you very much for your answer ! Apologies for this (!) but the thread has been duplicated there: https://www.biostars.org/p/140090/#140217   ...
written 4.2 years ago by AurelieMLB40

Latest awards to AurelieMLB

Great Question 4.1 years ago, created a question with more than 5,000 views. For Design formula and Design matrix in DESeq
Popular Question 4.1 years ago, created a question with more than 1,000 views. For DESeq2 normalisation: is the size of the gene taken into account?
Popular Question 4.1 years ago, created a question with more than 1,000 views. For Design formula and Design matrix in DESeq
Popular Question 4.1 years ago, created a question with more than 1,000 views. For Design formula and Design matrix in DESeq

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