User: Simon Anders

gravatar for Simon Anders
Simon Anders3.4k
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Location:
Zentrum für Molekularbiologie, Universität Heidelberg
Last seen:
1 week ago
Joined:
7 years, 10 months ago
Email:
s******@fs.tum.de

Posts by Simon Anders

<prev • 350 results • page 1 of 35 • next >
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Comment: C: deseq2 low read input
... What do you mean by "offset"? ...
written 7 days ago by Simon Anders3.4k
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Comment: C: DESeq2 unequal sample sizes
... You will have to tell us more about the biology of the experiment to get a good answer. Hence I start with a comment, or a question: Why do you think that looking for differences between A-Ctrl and B-Ctrl gives you an answer better fitting your biological question than simply comparing A to B? (Wha ...
written 13 days ago by Simon Anders3.4k
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Comment: C: Sample label swap in HTML results
... Please also post the relevant lines of your count tables that lead you to think that 'control' is expressed above 'resistant', and the output of sizeFactors(dxd)  ...
written 3 months ago by Simon Anders3.4k
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Comment: C: Sample label swap in HTML results
... Please post the complete R code that you used to get from the sample and count tables to the plot you posted. Thanks. ...
written 3 months ago by Simon Anders3.4k
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Comment: C: P values from Deseq Analysis
... No, you should not use DESeq on RPKM data. May I suggest at this point that you read the manual first before proceeding? Start here: https://www.bioconductor.org/help/workflows/rnaseqGene/ ...
written 5 months ago by Simon Anders3.4k
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Comment: C: P values from Deseq Analysis
... No. It is correct that a p=0.5 does not show that the gene is uninteresting, but that does not mean that it can still be worth reporting. A high p values simply says that the experiment failed to provide any new insight into the gene, and hence that you cannot draw any conclusions from that data. ...
written 5 months ago by Simon Anders3.4k
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Answer: A: P values from Deseq Analysis
... You don't have any significant genes. Remember the definition of a p-value: If you test N genes, and in reality, there are no differences at all, just random fluctuation, then, by definition of the p-value, you expect that pN genes show a p-value smaller then p (because p-values are supposed to hav ...
written 5 months ago by Simon Anders3.4k
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Job: PhD Position for computational scientist in Heidelberg
... The new group of Dr. Simon Anders at the Centre for Molecular Biology of the University of Heidelberg (ZMBH) is researching bioinformatics methodology for big data in molecular biology. We develop novel statistical inference methods for various types of high-throughput sequencing assays, and novel t ...
job computational biology bioinformatician job written 5 months ago by Simon Anders3.4k
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Comment: C: DESeq2: interaction term as in limma
... Not necessarily, because "absence of evidence is not evidence of absence" of an effect. So, if the p value for (B_ko-B_ctrl) is high, this could either mean that there is no effect or that the variance is too high to tell. Hence, seeing a significant p value for (A_ko-A_ctrl) but not for (B_ko-B_ct ...
written 6 months ago by Simon Anders3.4k
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Answer: A: DESeq2: interaction term as in limma
... Nearly correct. The last line should be: res <- results( dds, name="celltypeB.proteinko" )   Have a look at resultsNames: > resultsNames(dds) [1] "Intercept" "celltype_B_vs_A" "protein_ko_vs_control" [4] "celltypeB.proteinko"   Celltype_B_vs_A is the difference bet ...
written 6 months ago by Simon Anders3.4k

Latest awards to Simon Anders

Teacher 5 months ago, created an answer with at least 3 up-votes. For A: P values from Deseq Analysis
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Normalization methodology in DESeq/DESeq2 vs edgeR
Good Answer 10 months ago, created an answer that was upvoted at least 5 times. For A: DEXSeq Usage and Expression Confusion
Scholar 18 months ago, created an answer that has been accepted. For A: DEXSeq Usage and Expression Confusion
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: DESeq2 with paired samples - problem with the design
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: DEXSeq Usage and Expression Confusion
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: Normalization methodology in DESeq/DESeq2 vs edgeR
Scholar 18 months ago, created an answer that has been accepted. For A: DESeq2 with paired samples - problem with the design
Scholar 18 months 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 18 months ago, created an answer that has been accepted. For A: about DEseq for spike-in datasets
Scholar 18 months ago, created an answer that has been accepted. For A: Design: DESeq2 and continuous variables
Appreciated 18 months ago, created a post with more than 5 votes. For A: DEXSeq Usage and Expression Confusion
Student 21 months ago, asked a question with at least 3 up-votes. For looping through a GRangesList object
Commentator 22 months ago, created a comment with at least 3 up-votes. For C: Normalization methodology in DESeq/DESeq2 vs edgeR
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: Normalization methodology in DESeq/DESeq2 vs edgeR
Scholar 2.1 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: DEXSeq Usage and Expression Confusion
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: DEXSeq Usage and Expression Confusion
Good Answer 2.7 years ago, created an answer that was upvoted at least 5 times. For A: DEXSeq Usage and Expression Confusion
Appreciated 2.8 years ago, created a post with more than 5 votes. For A: DEXSeq Usage and Expression Confusion
Teacher 2.8 years ago, created an answer with at least 3 up-votes. For A: DEXSeq Usage and Expression Confusion
Scholar 2.8 years ago, created an answer that has been accepted. For A: DEXSeq Usage and Expression Confusion
Centurion 3.2 years ago, created 100 posts.

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