User: Simon Anders

gravatar for Simon Anders
Simon Anders3.3k
Reputation:
3,310
Status:
Trusted
Location:
Zentrum für Molekularbiologie, Universität Heidelberg
Last seen:
2 weeks ago
Joined:
7 years, 6 months ago
Email:
s******@fs.tum.de

Posts by Simon Anders

<prev • 346 results • page 1 of 35 • next >
0
votes
3
answers
186
views
3
answers
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 6 weeks ago by Simon Anders3.3k
0
votes
3
answers
186
views
3
answers
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 6 weeks ago by Simon Anders3.3k
0
votes
3
answers
186
views
3
answers
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 6 weeks ago by Simon Anders3.3k
2
votes
0
answers
186
views
0
answers
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 ...
0
votes
1
answers
144
views
1
answers
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 8 weeks ago by Simon Anders3.3k
0
votes
1
answers
144
views
1
answers
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 8 weeks ago by Simon Anders3.3k
0
votes
1
answers
315
views
1
answers
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 10 weeks ago by Simon Anders3.3k
0
votes
1
answers
315
views
1
answers
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 11 weeks ago by Simon Anders3.3k
0
votes
2
answers
253
views
2
answers
Answer: A: DESEq2 error when performing exploratory analysis with no replicates
... DESeq2 is a tool to test statistical hypotheses, i.e., to calculate p values to quantify how much evidence you have for differential evidence. As you don't have replicates, you can't have p values. For exploratory data analysis, you could consider using the "rlog" transformation and then just look ...
written 7 months ago by Simon Anders3.3k
0
votes
2
answers
222
views
2
answers
Answer: A: Design: DESeq2 and continuous variables
... There are several conceptually different questions you may want to ask: 1. For a given time point, and a given gene: Does the expression of the gene at this time point correlate with BMI? 2. For two time points and a given gene: Does the change in expression from the first to the second time point ...
written 7 months ago by Simon Anders3.3k

Latest awards to Simon Anders

Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: P values from Deseq Analysis
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: Normalization methodology in DESeq/DESeq2 vs edgeR
Good Answer 6 months ago, created an answer that was upvoted at least 5 times. For A: DEXSeq Usage and Expression Confusion
Scholar 14 months ago, created an answer that has been accepted. For A: DEXSeq Usage and Expression Confusion
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: DESeq2 with paired samples - problem with the design
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: DEXSeq Usage and Expression Confusion
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Normalization methodology in DESeq/DESeq2 vs edgeR
Scholar 14 months ago, created an answer that has been accepted. For A: DESeq2 with paired samples - problem with the design
Scholar 14 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 14 months ago, created an answer that has been accepted. For A: about DEseq for spike-in datasets
Scholar 14 months ago, created an answer that has been accepted. For A: Design: DESeq2 and continuous variables
Appreciated 14 months ago, created a post with more than 5 votes. For A: DEXSeq Usage and Expression Confusion
Student 17 months ago, asked a question with at least 3 up-votes. For looping through a GRangesList object
Commentator 18 months ago, created a comment with at least 3 up-votes. For C: Normalization methodology in DESeq/DESeq2 vs edgeR
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: Normalization methodology in DESeq/DESeq2 vs edgeR
Scholar 21 months ago, created an answer that has been accepted. For A: about DEseq for spike-in datasets
Teacher 23 months ago, created an answer with at least 3 up-votes. For A: DEXSeq Usage and Expression Confusion
Scholar 23 months ago, created an answer that has been accepted. For A: DEXSeq Usage and Expression Confusion
Scholar 23 months ago, created an answer that has been accepted. For A: DEXSeq Usage and Expression Confusion
Good Answer 2.4 years ago, created an answer that was upvoted at least 5 times. For A: DEXSeq Usage and Expression Confusion
Appreciated 2.5 years ago, created a post with more than 5 votes. For A: DEXSeq Usage and Expression Confusion
Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: DEXSeq Usage and Expression Confusion
Scholar 2.5 years ago, created an answer that has been accepted. For A: DEXSeq Usage and Expression Confusion
Centurion 2.9 years ago, created 100 posts.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 270 users visited in the last hour