User: Simon Anders

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Simon Anders3.6k
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Zentrum für Molekularbiologie, Universität Heidelberg
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Posts by Simon Anders

<prev • 385 results • page 3 of 39 • next >
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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 20 months ago by Simon Anders3.6k
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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 21 months ago by Simon Anders3.6k
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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$padj), ] ...
written 21 months ago by Simon Anders3.6k
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Comment: C: DESeq2 results export padj sorted
... You have:  bn_group_male_padj.1_sorted = bn_group_male_padj.1[order(bn_group_male_padj.1$padj<.1), ] I guess this is not what you meant. If you wanted to use "order", there shouldn't be "<.1". ...
written 21 months ago by Simon Anders3.6k
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Comment: C: Matrix not full rank - DESeq2
... Not quite. Your batch information seems to imply that, say, sample MMV1 might be much more similar to sample FMV1 than to sample FMV2. If this is in fact the case, you'd need to account for it to maintain type-I error control. However, accounting for this requires mixed-effect models, which DESeq2 d ...
written 21 months ago by Simon Anders3.6k
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Answer: A: Matrix not full rank - DESeq2
... You cannot use your batch information as it is nested in treatment. Try without. ...
written 21 months ago by Simon Anders3.6k
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Answer: A: Error: C stack usage when installing Txdb package
... On my system, updating the base packages solved the issue. (See: https://support.bioconductor.org/p/103995/#104087) ...
written 22 months ago by Simon Anders3.6k
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Comment: C: Error: C stack usage when installing Txdb package
... I managed to rid my system of the error. I had noticed that it has nothing to do with the annotation packages at all, because S4 as a whole was broken: The "C stack limit" error happened whenever I called any S4 method after loading GenomicFeatures. So, I updated all those base installation packages ...
written 22 months ago by Simon Anders3.6k
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Comment: C: Error: C stack usage when installing Txdb package
... I've just noticed that I had not yet updated to the newest Bioc release, so I just did a BiocUpgrade. However, the error persists. Also, the issue happens with other db packages, too. For example: If I run, in a fresh R session, "library( org.Hs.db.eg )", and then, "library( GenomicFeatures )", th ...
written 22 months ago by Simon Anders3.6k
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Comment: C: Error: C stack usage when installing Txdb package
... > BiocInstaller::biocValid() [1] TRUE > sessionInfo() R version 3.4.2 (2017-09-28) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 16.04.3 LTS Matrix products: default BLAS: /usr/lib/openblas-base/libblas.so.3 LAPACK: /usr/lib/libopenblasp-r0.2.18.so locale: [1] LC_CTYPE=en_U ...
written 22 months ago by Simon Anders3.6k

Latest awards to Simon Anders

Scholar 3 months ago, created an answer that has been accepted. For A: Design: DESeq2 and continuous variables
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: P values from Deseq Analysis
Popular Question 10 months ago, created a question with more than 1,000 views. For Deseq2 and differentia expression
Guru 12 months ago, received more than 100 upvotes.
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: P values from Deseq Analysis
Popular Question 14 months ago, created a question with more than 1,000 views. For PhD student and post-doctoral position (computational, molecular medicine)
Commentator 19 months ago, created a comment with at least 3 up-votes. For C: DESeq2: interaction term as in limma
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: P values from Deseq Analysis
Popular Question 2.4 years ago, created a question with more than 1,000 views. For PhD student and post-doctoral position (computational, molecular medicine)
Popular Question 2.4 years ago, created a question with more than 1,000 views. For looping through a GRangesList object
Popular Question 2.4 years ago, created a question with more than 1,000 views. For IlluminaHumanMethylation450k.db has undeclared dependency on AnnotationForge
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: P values from Deseq Analysis
Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: Normalization methodology in DESeq/DESeq2 vs edgeR
Good Answer 2.8 years ago, created an answer that was upvoted at least 5 times. For A: DEXSeq Usage and Expression Confusion
Scholar 3.5 years ago, created an answer that has been accepted. For A: about DEseq for spike-in datasets
Scholar 3.5 years ago, created an answer that has been accepted. For A: Design: DESeq2 and continuous variables
Appreciated 3.5 years ago, created a post with more than 5 votes. For A: DEXSeq Usage and Expression Confusion
Teacher 3.5 years ago, created an answer with at least 3 up-votes. For A: DESeq2 with paired samples - problem with the design
Scholar 3.5 years ago, created an answer that has been accepted. For A: DESeq2 with paired samples - problem with the design
Scholar 3.5 years ago, created an answer that has been accepted. For A: DEXSeq Usage and Expression Confusion
Scholar 3.5 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 3.5 years ago, created an answer with at least 3 up-votes. For A: DEXSeq Usage and Expression Confusion
Teacher 3.5 years ago, created an answer with at least 3 up-votes. For A: Normalization methodology in DESeq/DESeq2 vs edgeR
Student 3.7 years ago, asked a question with at least 3 up-votes. For looping through a GRangesList object
Teacher 3.8 years ago, created an answer with at least 3 up-votes. For A: Normalization methodology in DESeq/DESeq2 vs edgeR

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