User: Simon Anders

gravatar for Simon Anders
Simon Anders3.5k
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Zentrum für Molekularbiologie, Universität Heidelberg
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8 years, 8 months ago
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Posts by Simon Anders

<prev • 376 results • page 1 of 38 • next >
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Comment: C: DESeq2 Multi factor, multi time point comparison design formula
... If you want to know whether your comparisons make sense, you need to tell us more about the biology of your experiment. What is a "scafffold" and what do you want to find out about it? ...
written 5 days ago by Simon Anders3.5k
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Answer: A: RNA-seq data analysis with two species using DESeq2
... If you find significant differences between the samples with behaviour 4 and behaviour 1, you cannot say whether this difference is due to the fact that the samples are from animals exhibiting different behavior or due to the fact that they are different species. Your observation that PCA shows most ...
written 12 days ago by Simon Anders3.5k
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Comment: C: RNA-seq data analysis with two species using DESeq2
... Why are you surprised that species explains the bulk of the variance? Also: Please always post the sample table with such questions and explain how the samples differ. ...
written 14 days ago by Simon Anders3.5k
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Answer: A: should I get the logarithm of count values when I use standard method
... No, of course not! Why would you think that? (Background: The DESeq manual states, as explicitly as possible and since the very first version, that the matrix should contain "read counts", i.e., integer numbers that count how many reads map to the gene. Nevertheless, I have been asked hundreds of t ...
written 9 weeks ago by Simon Anders3.5k
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Answer: A: ASE using DESeq2
... The estimateSizeFactor function does not use the design information. You will get the same size factors, no matter what design formula you specify. So, your code does not do what you think it does. I could try to explain now how to do it correctly, but I guess Mike's write-up does tha job, so I let ...
written 9 weeks ago by Simon Anders3.5k
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Comment: C: DESeq2 result interpretation when adjusting for sex and age
... I'm not sure I understand your question but I guess, your problem is: What exactly do you mean with "considering age and sex" or "adjusted for age and sex"? Before I go into what is usually meant by these terms, another question: Do you have n subjects, each with three samples (control, treatment1, ...
written 5 months ago by Simon Anders3.5k
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Comment: C: Normalization by DEseq
... No, the normalized counts are calculated as raw counts divided by size factor. ...
written 5 months ago by Simon Anders3.5k
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Comment: C: Comparing between two differential expression analysis - two different fold chan
... Regarding your last question: First not that asking for difference in treatment success is somewhat different to asking for difference in gene expression, so let's stick to the latter. Now, if you see a gene that goes up much more strongly in men upon treatment A than in women upon treatment B, you ...
written 5 months ago by Simon Anders3.5k
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Comment: C: Requesting help with RNA-Seq differential gene analysis
... For many of your questions, the answer can be found in the vignette. Please give details n what you have already read, and wherev you had difficulty following, so that we don't have to start at zero with explanations. ...
written 5 months ago by Simon Anders3.5k
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Comment: C: Comparing between two differential expression analysis - two different fold chan
... Right. That's why I made an example sample table for myself to check, because I wasn't sure either. Turned out it's easier without interaction. ...
written 5 months ago by Simon Anders3.5k

Latest awards to Simon Anders

Teacher 4 months ago, created an answer with at least 3 up-votes. For A: P values from Deseq Analysis
Commentator 4 months ago, created a comment with at least 3 up-votes. For C: DESeq2: interaction term as in limma
Popular Question 14 months ago, created a question with more than 1,000 views. For IlluminaHumanMethylation450k.db has undeclared dependency on AnnotationForge
Popular Question 14 months ago, created a question with more than 1,000 views. For looping through a GRangesList object
Popular Question 14 months ago, created a question with more than 1,000 views. For PhD student and post-doctoral position (computational, molecular medicine)
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: P values from Deseq Analysis
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Normalization methodology in DESeq/DESeq2 vs edgeR
Good Answer 20 months ago, created an answer that was upvoted at least 5 times. For A: DEXSeq Usage and Expression Confusion
Appreciated 2.3 years ago, created a post with more than 5 votes. For A: DEXSeq Usage and Expression Confusion
Scholar 2.3 years ago, created an answer that has been accepted. For A: about DEseq for spike-in datasets
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: DESeq2 with paired samples - problem with the design
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: DEXSeq Usage and Expression Confusion
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: Normalization methodology in DESeq/DESeq2 vs edgeR
Scholar 2.3 years ago, created an answer that has been accepted. For A: DESeq2 with paired samples - problem with the design
Scholar 2.3 years ago, created an answer that has been accepted. For A: DEXSeq Usage and Expression Confusion
Scholar 2.3 years ago, created an answer that has been accepted. For A: DESEQ2 : When we merge technical replicates raw reads, do we need to divide by t
Scholar 2.3 years ago, created an answer that has been accepted. For A: Design: DESeq2 and continuous variables
Student 2.6 years ago, asked a question with at least 3 up-votes. For looping through a GRangesList object
Teacher 2.7 years ago, created an answer with at least 3 up-votes. For A: Normalization methodology in DESeq/DESeq2 vs edgeR
Commentator 2.7 years ago, created a comment with at least 3 up-votes. For C: Normalization methodology in DESeq/DESeq2 vs edgeR
Scholar 2.9 years ago, created an answer that has been accepted. For A: about DEseq for spike-in datasets
Teacher 3.1 years ago, created an answer with at least 3 up-votes. For A: DEXSeq Usage and Expression Confusion
Scholar 3.1 years ago, created an answer that has been accepted. For A: DEXSeq Usage and Expression Confusion
Scholar 3.1 years ago, created an answer that has been accepted. For A: DEXSeq Usage and Expression Confusion
Good Answer 3.5 years ago, created an answer that was upvoted at least 5 times. For A: DEXSeq Usage and Expression Confusion

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