User: Simon Anders

gravatar for Simon Anders
Simon Anders3.4k
Reputation:
3,420
Status:
Trusted
Location:
Zentrum für Molekularbiologie, Universität Heidelberg
Last seen:
1 day, 12 hours ago
Joined:
8 years, 1 month ago
Email:
s******@fs.tum.de

Posts by Simon Anders

<prev • 364 results • page 1 of 37 • next >
0
votes
1
answers
72
views
1
answers
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 1 day ago by Simon Anders3.4k
0
votes
1
answers
72
views
1
answers
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$padj), ] ...
written 1 day ago by Simon Anders3.4k
0
votes
1
answers
72
views
1
answers
Comment: C: DESeq2 results export padj sorted
... You have:  bn_group_male_padj.1_sorted = bn_group_male_padj.1[order(bn_group_male_padj.1$padj<.1), ] I guess this is not what you meant. If you wanted to use "order", there shouldn't be "<.1". ...
written 1 day ago by Simon Anders3.4k
0
votes
1
answers
79
views
1
answers
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 1 day ago by Simon Anders3.4k
0
votes
1
answers
79
views
1
answers
Answer: A: Matrix not full rank - DESeq2
... You cannot use your batch information as it is nested in treatment. Try without. ...
written 1 day ago by Simon Anders3.4k
0
votes
2
answers
140
views
2
answers
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 5 weeks ago by Simon Anders3.4k
0
votes
2
answers
140
views
2
answers
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 5 weeks ago by Simon Anders3.4k
0
votes
2
answers
140
views
2
answers
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 5 weeks ago by Simon Anders3.4k
0
votes
2
answers
140
views
2
answers
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 5 weeks ago by Simon Anders3.4k
0
votes
2
answers
140
views
2
answers
Comment: C: Error: C stack usage when installing Txdb package
... It's not the sqlite file. I've dug a bit deeper. Evidence points to the GenomicFeatures package. See here: I start with a fresh R session anders@merlot:~$ R R version 3.4.2 (2017-09-28) -- "Short Summer" I connect to the sqlite file: > conn <- AnnotationDbi::dbFileConnect( "tmp/TxDb.Hsap ...
written 5 weeks ago by Simon Anders3.4k

Latest awards to Simon Anders

Teacher 8 months ago, created an answer with at least 3 up-votes. For A: P values from Deseq Analysis
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Normalization methodology in DESeq/DESeq2 vs edgeR
Good Answer 13 months ago, created an answer that was upvoted at least 5 times. For A: DEXSeq Usage and Expression Confusion
Scholar 21 months ago, created an answer that has been accepted. For A: DEXSeq Usage and Expression Confusion
Teacher 21 months ago, created an answer with at least 3 up-votes. For A: DESeq2 with paired samples - problem with the design
Teacher 21 months ago, created an answer with at least 3 up-votes. For A: DEXSeq Usage and Expression Confusion
Teacher 21 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: DESeq2 with paired samples - problem with the design
Scholar 21 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 21 months ago, created an answer that has been accepted. For A: about DEseq for spike-in datasets
Scholar 21 months ago, created an answer that has been accepted. For A: Design: DESeq2 and continuous variables
Appreciated 21 months ago, created a post with more than 5 votes. For A: DEXSeq Usage and Expression Confusion
Student 24 months ago, asked a question with at least 3 up-votes. For looping through a GRangesList object
Commentator 2.1 years ago, created a comment with at least 3 up-votes. For C: Normalization methodology in DESeq/DESeq2 vs edgeR
Teacher 2.1 years ago, created an answer with at least 3 up-votes. For A: Normalization methodology in DESeq/DESeq2 vs edgeR
Scholar 2.3 years ago, created an answer that has been accepted. For A: about DEseq for spike-in datasets
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
Scholar 2.5 years ago, created an answer that has been accepted. For A: DEXSeq Usage and Expression Confusion
Good Answer 2.9 years ago, created an answer that was upvoted at least 5 times. For A: DEXSeq Usage and Expression Confusion
Appreciated 3.0 years ago, created a post with more than 5 votes. For A: DEXSeq Usage and Expression Confusion
Teacher 3.0 years ago, created an answer with at least 3 up-votes. For A: DEXSeq Usage and Expression Confusion
Scholar 3.0 years ago, created an answer that has been accepted. For A: DEXSeq Usage and Expression Confusion
Centurion 3.4 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: 286 users visited in the last hour