User: Jerry Cholo

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Jerry Cholo170
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Posts by Jerry Cholo

<prev • 18 results • page 1 of 2 • next >
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Analysis of Next Generation of Sequencing DAta
... Hello, I would like to use publicly available datasets (next generation of sequencing including both DNA and RNA sequencing data) associated to “ovarian cancer” existing in Sequence Read Archive (SRA) or any other resources. May someone let me know which package(s) is (are) available through Bioco ...
sradb written 3.1 years ago by Jerry Cholo170 • updated 3.1 years ago by Sean Davis21k
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Looking for a function
... ​Hello, In Bioconductor, I am looking for a function, in that the input of the function would be a word such as “inflammation”, “fibrosis”, or “apoptosis”, and the output of the function should be the list of significant “gene symbols” associated with the input words. The degr ...
written 3.6 years ago by Jerry Cholo170 • updated 3.6 years ago by Steve Lianoglou12k
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To get expression data from GEO
... Hello, I would like to have expression data for GSE27597. When I ran following command line: data1 = getGEO("GSE27597") I noticed that there are two files related to this GSE (see below): Found 2 file(s) GSE27597-GPL13243_series_matrix.txt.gz Using locally cached version: C:\Users\A ...
written 3.7 years ago by Jerry Cholo170 • updated 3.7 years ago by Vegard Nygaard100
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Surrogate Variable Analysis
... Hello, I would like to remove the batch effects from a gene expression data using Surrogate Variable Analysis (SVA). When I looked at the SVA ( http://www.bioconductor.org/packages/release/bioc/html/sva.html) and "bladderbatch", I noticed that for 57 different samples, there are 5 different batche ...
sva written 3.7 years ago by Jerry Cholo170 • updated 3.7 years ago by Jeff Leek490
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package 'impute' is not available (for R version 3.0.2)
... Hello, install.packages('impute') Warning message: package 'impute' is not available (for R version 3.0.2) May someone let me know how I could this problem? Thanks, Jerry [[alternative HTML version deleted]] ...
written 3.7 years ago by Jerry Cholo170 • updated 3.7 years ago by Levi Waldron380
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Filter out genes with small profile variance from gene expression data
... Hello, The following are the command lines that I have been using to filter out genes with small profile variance from gene expression data by Matlab. ---------------------------------------------------------------------- % filter genes with small profile variance % less than 25 percentile ...
written 3.7 years ago by Jerry Cholo170 • updated 3.7 years ago by Martin Morgan ♦♦ 20k
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getGEO
... Hello, I need to extract this txt file. When I used following command line: Data_GPL5571 <- read.table('GSE27634-GPL5571_series_matrix.txt.gz') I got this error: Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, : line 46 did not have 2 elements Thanks, Jerry ...
written 3.7 years ago by Jerry Cholo170 • updated 3.7 years ago by Sean Davis21k
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Get eset from GLP
... Hello, May someone let me know how I could get "eset" or "Expression Set" for a GLP data? gpl<- getGEO(filename='GPL570.soft') Thanks, Jerry [[alternative HTML version deleted]] ...
written 3.7 years ago by Jerry Cholo170
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Error in x[["Version"]] : subscript out of bounds
... Hello, I ran this line: > sft=pickSoftThreshold(datExprFemale,powerVector=powers) I got this error: Error in { : task 1 failed - ""corFast" not available for .C() for package "WGCNA"" Here is: > sessionInfo() ---------------------------------------------------------------------- ------ ...
written 3.8 years ago by Jerry Cholo170
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WGCNA
... Hello, When I ran this line: > sft=pickSoftThreshold(datExprFemale,powerVector=powers) I got this error: Error in { : task 1 failed - ""corFast" not available for .C() for package "WGCNA"" May someone let me know how I could fix it? Thanks, Jerry [[alternative HTML version deleted ...
written 3.8 years ago by Jerry Cholo170 • updated 3.8 years ago by Peter Langfelder1.3k

Latest awards to Jerry Cholo

Popular Question 3.1 years ago, created a question with more than 1,000 views. For package 'impute' is not available (for R version 3.0.2)
Popular Question 3.1 years ago, created a question with more than 1,000 views. For package 'impute' is not available (for R version 3.0.2)

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