User: Simon Anders

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Simon Anders3.6k
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Zentrum für Molekularbiologie, Universität Heidelberg
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Joined:
9 years, 8 months ago
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Posts by Simon Anders

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Answer: A: TMM Normalization: DESeqDataSet: some values in assay are negative
... Your question is asked quite often, strangely enough, so let me first repeat our standard answer: DESeq2 wants **raw** **unnormalized** counts. Do not supply anything else, ever. Obviously, the easiest would be to to run the whole analysis (normalization and DE testing) using either only edgeR or ...
written 4 weeks ago by Simon Anders3.6k
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Comment: C: Paired samples in cell lines using DESeq2
... I have to disagree with ATpoint here. It is actually a good design to use cell lines derived from multiple patients. This assures that the list of differentially expressed genes that OP will find is not specific to one (arbitrarily chosen) patient but has some generality and hence likely to have goo ...
written 5 weeks ago by Simon Anders3.6k
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Answer: A: DEXSeq error in dexseq_count.py. ValueError: need more than 4 values to unpack
... In your call to dexseq_count.py, you should first give the name of the GFF file, and only after that list the BAM files. So, it should be ``` python2.7 /usr/local/lib/R/site-library/DEXSeq/python_scripts/dexseq_count.py -p yes -r name -a 10 -s no -f bam ./Arabidopsis_thaliana.TAIR10.42.DEXSeq.gff ...
written 7 weeks ago by Simon Anders3.6k
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Comment: C: Genes that have NOT changed
... Have you copied all code from the old post verbatim (without *any* changes), or have you adapted it to your data? If the latter, please post the *full* code. ...
written 8 months ago by Simon Anders3.6k
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Job: applied methods development for single-cell sequencing
... At Heidelberg University, we have vacancies for 1 PhD student and 2 post-doc positions for computational scientists with skills in data science, statistics or bioinformatics. All three positions are related to projects applying single-cell sequencing techniques to questions of human biology, name ...
job computational biology single-cell written 8 months ago by Simon Anders3.6k
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Comment: C: p-values smaller than machine epsilon in DESeq2
... Or, to answer the second question very directly: Not at all. A very low p value means that either model asumption is wrong or the evidence against the null hypothesis with almost certainty. There is little point in seeing different levels between being almost certain. This is why I usually recomme ...
written 9 months ago by Simon Anders3.6k
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Comment: C: DESeq2 Time Series and "control" condition
... try results( dds, contrast = c( "Age", "M18", "M12" ) ...
written 10 months ago by Simon Anders3.6k • updated 10 months ago by Michael Love24k
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Job: PhD opportunity in Heidelberg for computational people
... We are looking for a talented and motivated PhD Student with computational expertise for a project on the use of single-cell transcriptomics on cancer samples at Heidelberg University / Heidelberg University Hospital / EMBL-MMPU. For more information, please see here. ...
job single-cell phd position written 10 months ago by Simon Anders3.6k
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Answer: A: latest version of R is 3.5.1 and it does not compatible with many Bioconductor p
... Do not use 'install.packages'. Instead, follow the installation instructions for Bioconductor: https://www.bioconductor.org/install/   ...
written 12 months ago by Simon Anders3.6k
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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 12 months ago by Simon Anders3.6k

Latest awards to Simon Anders

Scholar 4 weeks ago, created an answer that has been accepted. For A: Design: DESeq2 and continuous variables
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: P values from Deseq Analysis
Popular Question 8 months ago, created a question with more than 1,000 views. For Deseq2 and differentia expression
Guru 10 months ago, received more than 100 upvotes.
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: P values from Deseq Analysis
Popular Question 12 months ago, created a question with more than 1,000 views. For PhD student and post-doctoral position (computational, molecular medicine)
Commentator 17 months ago, created a comment with at least 3 up-votes. For C: DESeq2: interaction term as in limma
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: P values from Deseq Analysis
Popular Question 2.2 years ago, created a question with more than 1,000 views. For PhD student and post-doctoral position (computational, molecular medicine)
Popular Question 2.2 years ago, created a question with more than 1,000 views. For looping through a GRangesList object
Popular Question 2.2 years ago, created a question with more than 1,000 views. For IlluminaHumanMethylation450k.db has undeclared dependency on AnnotationForge
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: P values from Deseq Analysis
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: Normalization methodology in DESeq/DESeq2 vs edgeR
Good Answer 2.7 years ago, created an answer that was upvoted at least 5 times. For A: DEXSeq Usage and Expression Confusion
Scholar 3.4 years ago, created an answer that has been accepted. For A: about DEseq for spike-in datasets
Scholar 3.4 years ago, created an answer that has been accepted. For A: Design: DESeq2 and continuous variables
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: DESeq2 with paired samples - problem with the design
Scholar 3.4 years ago, created an answer that has been accepted. For A: DESeq2 with paired samples - problem with the design
Scholar 3.4 years ago, created an answer that has been accepted. For A: DEXSeq Usage and Expression Confusion
Scholar 3.4 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 3.4 years ago, created an answer with at least 3 up-votes. For A: DEXSeq Usage and Expression Confusion
Teacher 3.4 years ago, created an answer with at least 3 up-votes. For A: Normalization methodology in DESeq/DESeq2 vs edgeR
Student 3.6 years ago, asked a question with at least 3 up-votes. For looping through a GRangesList object
Teacher 3.7 years ago, created an answer with at least 3 up-votes. For A: Normalization methodology in DESeq/DESeq2 vs edgeR

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