Moderator: Sean Davis

gravatar for Sean Davis
Sean Davis21k
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21,000
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United States
Website:
http://watson.nci.nih....
Twitter:
@seandavis12
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Google Scholar Page
Last seen:
1 week ago
Joined:
10 years, 4 months ago
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Posts by Sean Davis

<prev • 2,146 results • page 1 of 215 • next >
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Comment: C: Processing two-colour array data from GEO using limma when no raw data are avail
... 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 7 days ago by Sean Davis21k
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Comment: C: question about getGEO function
... Could you attach the output of `sessionInfo()` after loading GEOquery? ...
written 8 days ago by Sean Davis21k
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Comment: C: Using eset while parsing GSE file located in a path
... The behavior you are seeing appears to be specific to your environment, so I do not really have a good set of suggestions other than to experiment. You might benefit from getting some local IT support to work with you.  ...
written 6 weeks ago by Sean Davis21k
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Comment: C: Using eset while parsing GSE file located in a path
... Looks like GEOquery is working correctly--not sure why it is slower. You could try using a smaller GSE (GSE20, maybe) to see if the process completes. If you are running in two different settings, file system performance and memory limitations may impact speed of processing, but now I am speculating ...
written 6 weeks ago by Sean Davis21k
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Comment: C: Using eset while parsing GSE file located in a path
... See the help for getGEO. In particular, if you set `destdir` in your script, the files will be downloaded only once. The second time the cached file is used. If you do not set `destdir`, a temporary directory is used and that temporary directory only lasts as long as R runs. ...
written 6 weeks ago by Sean Davis21k
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Answer: A: Using eset while parsing GSE file located in a path
... Parsing a SOFT format GSE will result in a GSE object. It is up to you, then, to parse out the information as needed. See https://bioconductor.org/packages/release/bioc/vignettes/GEOquery/inst/doc/GEOquery.html#converting-gse-to-an-expressionset. The GSE SOFT parsing functionality is historical and ...
written 6 weeks ago by Sean Davis21k
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Comment: C: Filtering the probe set ids from GSE file
... I'm not sure what is going on. This is what I see:  > gse = getGEO('GSE15543')[[1]] Found 1 file(s) GSE15543_series_matrix.txt.gz trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE15nnn/GSE15543/matrix/GSE15543_series_matrix.txt.gz' Content type 'application/x-gzip' length 14491926 bytes ( ...
written 6 weeks ago by Sean Davis21k
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Comment: C: Filtering Gene Symbols and Sample Description from GSE files of GEO
... Great to hear that things are working for you.  ...
written 6 weeks ago by Sean Davis21k
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Comment: C: Filtering Gene Symbols and Sample Description from GSE files of GEO
... Sorry, one more favor. Could you post the code you used to get `eset`? I'm assuming that it is a one-liner, but just double-checking.  ...
written 6 weeks ago by Sean Davis21k
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Comment: C: Filtering Gene Symbols and Sample Description from GSE files of GEO
... What is the output of sessionInfo() when GEOquery is loaded? And what is the output of just typing `eset`? ...
written 7 weeks ago by Sean Davis21k

Latest awards to Sean Davis

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 3 months ago, created an answer that has been accepted. For A: Using eset while parsing GSE file located in a path
Popular Question 4 months ago, created a question with more than 1,000 views. For Orchestrating a small, parallel, RNA-seq pre-processing workflow using R
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: GEOquery: 0 features in the gset object
Teacher 18 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?
Appreciated 18 months ago, created a post with more than 5 votes. For Invitation to submit articles to the Bioconductor gateway on F1000Research
Appreciated 18 months ago, created a post with more than 5 votes. For Accessing Public Genomic Data from Bioconductor
Popular Question 18 months ago, created a question with more than 1,000 views. For Illumina Expression analysis from iDAT files
Guru 18 months ago, received more than 100 upvotes.
Scholar 18 months ago, created an answer that has been accepted. For A: SummarizedExperiment object from GEOquery obtained GSE
Scholar 18 months ago, created an answer that has been accepted. For A: Are two biological replicates enough for a transcriptome analysis using DESeq2?
Scholar 18 months ago, created an answer that has been accepted. For A: GEOquery Fails to Download Series Matrix File
Scholar 18 months ago, created an answer that has been accepted. For A: getGEO Error: Duplicate identifiers for rows
Scholar 18 months ago, created an answer that has been accepted. For C: getGEO error when trying to download a series matrix file
Scholar 18 months ago, created an answer that has been accepted. For A: SRAdb: could not find function "sqliteTableFields"
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: SummarizedExperiment object from GEOquery obtained GSE
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: Adding a column to phenoData dataframe
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: GEOquery Fails to Download Series Matrix File
Appreciated 18 months ago, created a post with more than 5 votes. For Bioconductor packages now each have a DOI.
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: GEOquery Fails to Download Series Matrix File
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Illumina Expression analysis from iDAT files
Scholar 2.5 years ago, created an answer that has been accepted. For A: GEOquery Fails to Download Series Matrix File
Popular Question 2.5 years ago, created a question with more than 1,000 views. For dplyr and the GEOmetadb package for mining NCBI GEO metadata
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Accessing Public Genomic Data from Bioconductor
Appreciated 2.5 years ago, created a post with more than 5 votes. For Bootstrap confidence intervals on RNA-seq expression from Kallisto

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