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, 6 months ago
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Posts by Simon Anders

<prev • 373 results • page 1 of 38 • next >
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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 11 days 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 12 days 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 3 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 3 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 3 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 3 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 4 months ago by Simon Anders3.5k
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Answer: A: Comparing between two differential expression analysis - two different fold chan
... Hi Marina Mike must have overlooked that you have two different sets of patients, and each patient only gets either treatment "A" or treatment "B". An interaction would be needed if you had the both treatment applied to the same patient, but in your case, it is actually straightforward. I use the ...
written 4 months ago by Simon Anders3.5k
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Comment: C: Errors of loading HilbertVisGUI
... Judging from the path, your HlbertVisGUI DLL might be a 64 bit version (the path contains "x64") but it expects a 32 bit version. Maybe try installing the 64-bit version of gtkmm. See here: http://ftp.gnome.org/pub/GNOME/binaries/ Also, which R do you have? (Always incluse the output of sessionInfo ...
written 4 months ago by Simon Anders3.5k
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Comment: C: DESeq2 results export padj sorted
... I know. But you put the "<.1" into the parantheses after "order". So what happens is that the argument of order gets transformed into a vector of only TRUE and FALSE. The actual values of padj vanish. So, the ordering only ensures that FALSE comes before TRUE.  Now, as you have already filtered, ...
written 5 months ago by Simon Anders3.5k

Latest awards to Simon Anders

Popular Question 12 months ago, created a question with more than 1,000 views. For PhD student and post-doctoral position (computational, molecular medicine)
Popular Question 12 months ago, created a question with more than 1,000 views. For IlluminaHumanMethylation450k.db has undeclared dependency on AnnotationForge
Popular Question 12 months ago, created a question with more than 1,000 views. For looping through a GRangesList object
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: P values from Deseq Analysis
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Normalization methodology in DESeq/DESeq2 vs edgeR
Good Answer 18 months ago, created an answer that was upvoted at least 5 times. For A: DEXSeq Usage and Expression Confusion
Scholar 2.2 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
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: DESeq2 with paired samples - problem with the design
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: DEXSeq Usage and Expression Confusion
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: Normalization methodology in DESeq/DESeq2 vs edgeR
Scholar 2.2 years ago, created an answer that has been accepted. For A: DESeq2 with paired samples - problem with the design
Scholar 2.2 years ago, created an answer that has been accepted. For A: DEXSeq Usage and Expression Confusion
Scholar 2.2 years ago, created an answer that has been accepted. For A: about DEseq for spike-in datasets
Scholar 2.2 years ago, created an answer that has been accepted. For A: Design: DESeq2 and continuous variables
Appreciated 2.2 years ago, created a post with more than 5 votes. For A: DEXSeq Usage and Expression Confusion
Student 2.4 years ago, asked a question with at least 3 up-votes. For looping through a GRangesList object
Commentator 2.5 years ago, created a comment with at least 3 up-votes. For C: Normalization methodology in DESeq/DESeq2 vs edgeR
Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: Normalization methodology in DESeq/DESeq2 vs edgeR
Scholar 2.7 years ago, created an answer that has been accepted. For A: about DEseq for spike-in datasets
Teacher 2.9 years ago, created an answer with at least 3 up-votes. For A: DEXSeq Usage and Expression Confusion
Scholar 2.9 years ago, created an answer that has been accepted. For A: DEXSeq Usage and Expression Confusion
Scholar 2.9 years ago, created an answer that has been accepted. For A: DEXSeq Usage and Expression Confusion
Good Answer 3.3 years ago, created an answer that was upvoted at least 5 times. For A: DEXSeq Usage and Expression Confusion
Appreciated 3.4 years ago, created a post with more than 5 votes. For A: DEXSeq Usage and Expression Confusion
Teacher 3.4 years ago, created an answer with at least 3 up-votes. For A: DEXSeq Usage and Expression Confusion

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