User: Simon Anders

gravatar for Simon Anders
Simon Anders3.4k
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Zentrum für Molekularbiologie, Universität Heidelberg
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1 week, 1 day ago
Joined:
7 years, 8 months ago
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Posts by Simon Anders

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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 7 weeks 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 7 weeks 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 3 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 3 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 3 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 3 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 3 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 3 months ago by Simon Anders3.4k
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Comment: C: standard error value (lfcSE) returned by DeSeq2
... DESeq2's variance model assumes that all conditions have the same variance. This is a standard assumption in ANOVA that simplifies the math and substantially improves power (if the assumption is justified).  Hence, your approach will give you the same value for each condition. Any differences will ...
written 4 months ago by Simon Anders3.4k
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Comment: C: standard error value (lfcSE) returned by DeSeq2
... This sounds like you want to see whether one condition is more noisy then the other. If so, the answer is: no, you cannot get anything like a variance estimate per condition from the reported standard errors because DESeq2 does not calculate condition-specific variances. If you would write what (bi ...
written 4 months ago by Simon Anders3.4k

Latest awards to Simon Anders

Teacher 3 months ago, created an answer with at least 3 up-votes. For A: P values from Deseq Analysis
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Normalization methodology in DESeq/DESeq2 vs edgeR
Good Answer 8 months ago, created an answer that was upvoted at least 5 times. For A: DEXSeq Usage and Expression Confusion
Scholar 16 months ago, created an answer that has been accepted. For A: DEXSeq Usage and Expression Confusion
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: DESeq2 with paired samples - problem with the design
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: DEXSeq Usage and Expression Confusion
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: Normalization methodology in DESeq/DESeq2 vs edgeR
Scholar 16 months ago, created an answer that has been accepted. For A: DESeq2 with paired samples - problem with the design
Scholar 16 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 16 months ago, created an answer that has been accepted. For A: about DEseq for spike-in datasets
Scholar 16 months ago, created an answer that has been accepted. For A: Design: DESeq2 and continuous variables
Appreciated 16 months ago, created a post with more than 5 votes. For A: DEXSeq Usage and Expression Confusion
Student 19 months ago, asked a question with at least 3 up-votes. For looping through a GRangesList object
Commentator 20 months ago, created a comment with at least 3 up-votes. For C: Normalization methodology in DESeq/DESeq2 vs edgeR
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: Normalization methodology in DESeq/DESeq2 vs edgeR
Scholar 23 months ago, created an answer that has been accepted. For A: about DEseq for spike-in datasets
Teacher 2.1 years ago, created an answer with at least 3 up-votes. For A: DEXSeq Usage and Expression Confusion
Scholar 2.1 years ago, created an answer that has been accepted. For A: DEXSeq Usage and Expression Confusion
Scholar 2.1 years ago, created an answer that has been accepted. For A: DEXSeq Usage and Expression Confusion
Good Answer 2.5 years ago, created an answer that was upvoted at least 5 times. For A: DEXSeq Usage and Expression Confusion
Appreciated 2.6 years ago, created a post with more than 5 votes. For A: DEXSeq Usage and Expression Confusion
Teacher 2.6 years ago, created an answer with at least 3 up-votes. For A: DEXSeq Usage and Expression Confusion
Scholar 2.6 years ago, created an answer that has been accepted. For A: DEXSeq Usage and Expression Confusion
Centurion 3.0 years ago, created 100 posts.

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