Moderator: Sean Davis
Sean Davis ♦ 21k
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Posts by Sean Davis
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C: GEOquery:Get error sampleNames
... Just a quick update--the Rstudio team has a working fix and it is going through code review. Once that is completed and the new readr package is released, the GEOquery problem will be resolved.
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written 4 days ago by
Sean Davis ♦ 21k
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C: GEOQuery bug, NCBI or package?
... Just a quick update--the Rstudio team has a working fix and it is going through code review. Once that is completed and the new readr package is released, the GEOquery problem will be resolved.
...
written 4 days ago by
Sean Davis ♦ 21k
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C: GEOQuery bug, NCBI or package?
... This is a bug due to a change in behavior of the readr read_tsv function. https://github.com/tidyverse/readr/issues/925. There is an ongoing conversation about what to do here. Sorry for the instability.
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written 10 days ago by
Sean Davis ♦ 21k
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Comment:
C: GEOquery:Get error sampleNames
... Yes, the "bug" here is a change in behavior of read_tsv and friends in readr. See https://github.com/tidyverse/readr/issues/925.
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written 10 days ago by
Sean Davis ♦ 21k
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Comment:
C: GEOquery:Get error sampleNames
... Looks like a bug to me. I filed an issue (https://github.com/seandavi/GEOquery/issues/75).
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written 12 days ago by
Sean Davis ♦ 21k
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... Just a note that in the most recent devel version (1.5.8) of GenomicDataCommons, filter chaining is now supported. Each filter in the %>% chain is "AND"ed with the previous filters.
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written 6 weeks ago by
Sean Davis ♦ 21k
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... Thankfully, we have all the power of R at our disposal!
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written 6 weeks ago by
Sean Davis ♦ 21k
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... I don't think that the API supports that query. Instead, simply do two separate queries, get the case ids(), and intersect them. Then, perform a third cases() query and supply the ids().
> qCases1 <- cases() %>%
+ filter( ~ (samples.sample_type == "Solid Tissue Normal" | samples. ...
written 6 weeks ago by
Sean Davis ♦ 21k
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... There is a sort of unusual issue with using pipes (%>%) and filter. Unlike in dplyr, applying a second filter clears the first. I should definitely change this behavior, but in the meantime I think what you are looking for is:
qCases <- cases() %>%
filter( ~ (samples.sample_type == "Sol ...
written 6 weeks ago by
Sean Davis ♦ 21k
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... It would be best to spend some time reading the documentation for limma. If you have specific questions after going through the limma vignette, consider asking a new question rather than commenting on old questions.
...
written 8 weeks ago by
Sean Davis ♦ 21k
Latest awards to Sean Davis
Popular Question
6 weeks ago,
created a question with more than 1,000 views.
For Orchestrating a small, parallel, RNA-seq pre-processing workflow using R
Popular Question
3 months ago,
created a question with more than 1,000 views.
For dplyr and the GEOmetadb package for mining NCBI GEO metadata
Scholar
3 months ago,
created an answer that has been accepted.
For A: Filtering Gene Symbols and Sample Description from GSE files of GEO
Scholar
4 months ago,
created an answer that has been accepted.
For A: Filtering Gene Symbols and Sample Description from GSE files of GEO
Scholar
4 months ago,
created an answer that has been accepted.
For A: Using eset while parsing GSE file located in a path
Popular Question
6 months ago,
created a question with more than 1,000 views.
For Orchestrating a small, parallel, RNA-seq pre-processing workflow using R
Scholar
20 months ago,
created an answer that has been accepted.
For A: SummarizedExperiment object from GEOquery obtained GSE
Scholar
20 months ago,
created an answer that has been accepted.
For A: Are two biological replicates enough for a transcriptome analysis using DESeq2?
Scholar
20 months ago,
created an answer that has been accepted.
For A: GEOquery Fails to Download Series Matrix File
Scholar
20 months ago,
created an answer that has been accepted.
For A: getGEO Error: Duplicate identifiers for rows
Scholar
20 months ago,
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For C: getGEO error when trying to download a series matrix file
Scholar
20 months ago,
created an answer that has been accepted.
For A: SRAdb: could not find function "sqliteTableFields"
Teacher
20 months ago,
created an answer with at least 3 up-votes.
For A: SummarizedExperiment object from GEOquery obtained GSE
Teacher
20 months ago,
created an answer with at least 3 up-votes.
For A: Adding a column to phenoData dataframe
Teacher
20 months ago,
created an answer with at least 3 up-votes.
For A: GEOquery Fails to Download Series Matrix File
Teacher
20 months ago,
created an answer with at least 3 up-votes.
For A: How to check the read length for all the TCGA data samples in GDC?
Teacher
20 months ago,
created an answer with at least 3 up-votes.
For A: GEOquery: 0 features in the gset object
Appreciated
20 months ago,
created a post with more than 5 votes.
For Bioconductor packages now each have a DOI.
Appreciated
20 months ago,
created a post with more than 5 votes.
For Invitation to submit articles to the Bioconductor gateway on F1000Research
Appreciated
20 months ago,
created a post with more than 5 votes.
For Accessing Public Genomic Data from Bioconductor
Popular Question
20 months ago,
created a question with more than 1,000 views.
For Illumina Expression analysis from iDAT files
Guru
20 months ago,
received more than 100 upvotes.
Teacher
21 months ago,
created an answer with at least 3 up-votes.
For A: GEOquery Fails to Download Series Matrix File
Popular Question
2.6 years ago,
created a question with more than 1,000 views.
For Accessing Public Genomic Data from Bioconductor
Appreciated
2.6 years ago,
created a post with more than 5 votes.
For Bootstrap confidence intervals on RNA-seq expression from Kallisto
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