User: Simon Anders

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Simon Anders3.4k
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Zentrum für Molekularbiologie, Universität Heidelberg
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Posts by Simon Anders

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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 7 weeks ago by Simon Anders3.4k
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Comment: C: Normalization by DEseq
... No, the normalized counts are calculated as raw counts divided by size factor. ...
written 7 weeks ago by Simon Anders3.4k
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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 7 weeks ago by Simon Anders3.4k
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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 8 weeks ago by Simon Anders3.4k
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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 9 weeks ago by Simon Anders3.4k
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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 9 weeks ago by Simon Anders3.4k
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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 11 weeks ago by Simon Anders3.4k
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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 3 months ago by Simon Anders3.4k
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Comment: C: DESeq2 results export padj sorted
... It doesn't work that they. (You should have indicated that you are a novice R user.) You first subset, and then you sort: bn_group_male_padj.1 <- subset(bn_group_male, padj<.1) bn_group_male_padj.1_sorted = bn_group_male_padj.1[order(bn_group_male_padj.1$padj), ] ...
written 3 months ago by Simon Anders3.4k
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Comment: C: DESeq2 results export padj sorted
... You have:  bn_group_male_padj.1_sorted = bn_group_male_padj.1[order(bn_group_male_padj.1$padj<.1), ] I guess this is not what you meant. If you wanted to use "order", there shouldn't be "<.1". ...
written 3 months ago by Simon Anders3.4k

Latest awards to Simon Anders

Teacher 11 months ago, created an answer with at least 3 up-votes. For A: P values from Deseq Analysis
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Normalization methodology in DESeq/DESeq2 vs edgeR
Good Answer 16 months ago, created an answer that was upvoted at least 5 times. For A: DEXSeq Usage and Expression Confusion
Scholar 2.0 years ago, created an answer that has been accepted. For A: DEXSeq Usage and Expression Confusion
Teacher 2.0 years ago, created an answer with at least 3 up-votes. For A: DESeq2 with paired samples - problem with the design
Teacher 2.0 years ago, created an answer with at least 3 up-votes. For A: DEXSeq Usage and Expression Confusion
Teacher 2.0 years ago, created an answer with at least 3 up-votes. For A: Normalization methodology in DESeq/DESeq2 vs edgeR
Scholar 2.0 years ago, created an answer that has been accepted. For A: DESeq2 with paired samples - problem with the design
Scholar 2.0 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
Scholar 2.0 years ago, created an answer that has been accepted. For A: about DEseq for spike-in datasets
Scholar 2.0 years ago, created an answer that has been accepted. For A: Design: DESeq2 and continuous variables
Appreciated 2.0 years ago, created a post with more than 5 votes. For A: DEXSeq Usage and Expression Confusion
Student 2.2 years ago, asked a question with at least 3 up-votes. For looping through a GRangesList object
Commentator 2.3 years ago, created a comment with at least 3 up-votes. For C: Normalization methodology in DESeq/DESeq2 vs edgeR
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: Normalization methodology in DESeq/DESeq2 vs edgeR
Scholar 2.6 years ago, created an answer that has been accepted. For A: about DEseq for spike-in datasets
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
Scholar 2.8 years ago, created an answer that has been accepted. For A: DEXSeq Usage and Expression Confusion
Good Answer 3.2 years ago, created an answer that was upvoted at least 5 times. For A: DEXSeq Usage and Expression Confusion
Appreciated 3.3 years ago, created a post with more than 5 votes. For A: DEXSeq Usage and Expression Confusion
Teacher 3.3 years ago, created an answer with at least 3 up-votes. For A: DEXSeq Usage and Expression Confusion
Scholar 3.3 years ago, created an answer that has been accepted. For A: DEXSeq Usage and Expression Confusion
Centurion 3.7 years ago, created 100 posts.

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