User: Ying Chen

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Ying Chen110
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Posts by Ying Chen

<prev • 11 results • page 1 of 2 • next >
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Answer: A: ggvis: interactive heatmaps
... You'd better ask Winston Chang at ggvis google group (https://groups.google.com/forum/?hl=en#!forum/ggvis) directly, although he is kind dormant for the last couple of days :). Ying -----Original Message----- From: bioconductor-bounces@r-project.org [mailto:bioconductor- bounces@r-project.org] On ...
written 5.2 years ago by Ying Chen110
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affy( ) error with mas5()
... Hi guys, I use affy to process over 3800 affy U133Plus2 arrays. rma() went well, but mas5() gave me the error during background correcting: Error in matrix(.C("affy_background_adjust_R", as.double(as.vector(allintensities)), : long vectors (argument 1) are not supported in .Fortr ...
snp affy process written 5.5 years ago by Ying Chen110 • updated 5.5 years ago by James W. MacDonald51k
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GEOquery error when retrieving raw files
... Hi guys, I tried to use GEOquery to retrieve raw file, but got "No supplemental files found". > a <- getGEOSuppFiles("GSM528276", makeDirectory = TRUE, baseDir = getwd()) [1] "ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528276/suppl/" No supplemental files fou ...
geoquery written 5.7 years ago by Ying Chen110 • updated 5.7 years ago by Sean Davis21k
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SVA package error message: Error in diag(dims[2]) - mod %*% solve(t(mod) %*% mod) %*% t(mod) : non-conformable arrays
... Hi guys, I tried to use SVA package to identify number of batch factors in my gene expression dataset. But I ran into an error message: > library(sva) > load("myeset.RData") > pheno <- pData(myeset) > str(pheno) 'data.frame': 821 obs. of 4 variables: $ sample : Factor w/ 821 l ...
sva written 6.2 years ago by Ying Chen110
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Comment: C: How to set up genes argument for makeTranscriptDb( ) function in GenomicFeatures
... Hi Marc, Thanks a lot for the help. I start with GAF because I look at TCGA CRC data. Here was what I did initially: > library(GenomicFeatures) > library(GenomicRanges) > library(TxDb.Hsapiens.UCSC.hg19.knownGene) > TCGA_CRC <- read.delim("TCGA_CRC_UNC_RNASeq_ExonID_detail_new.txt ...
written 7.0 years ago by Ying Chen110
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Answer: A: How to set up genes argument for makeTranscriptDb( ) function in GenomicFeatures
... Sorry, one more question regarding the transcripts argument: For the following two transcripts: uc001aaa.3 chr1:11874-12227,12613-12721,13221-14409:+ uc010nxq.1 chr1:11874-12227,12595-12721,13403-14409:+ What should be the format for tx_start and tx_end? transcripts < ...
written 7.0 years ago by Ying Chen110
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How to set up genes argument for makeTranscriptDb( ) function in GenomicFeatures?
... Hi guys, I am new to the GenomicsFeatures package and I am trying to make my own txdb out of TCGA GAF file using the function makeTranscriptDb(transcripts, splicings,genes) in GenomicsFeatures. The manual says that genes is a data frame containing the genes associated to a set of transcripts. I jus ...
written 7.0 years ago by Ying Chen110
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Answer: A: Reading 5000 celfiles with ReadAffy
... Hi, You can try aroma.affymetrix, which is not a Bioconductor package yet. Or you can try the stand alone application RMAexpress as someone said he did a RMA on more than 10,000 cels with it. Ying -----Original Message----- From: bioconductor-bounces@r-project.org [mailto:bioconductor- bounces@r- ...
written 7.7 years ago by Ying Chen110
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Comment: C: sva package for R 2.13.1?
... Hi Sean, thanks a lot for the suggestion. I went to your afternoon talk at the BioC2011 and I learned a lot. Anyway I figured out how to install it using the source file I downloaded from Jeffry Leek's website. My computer runs windows 7 so I already have ActiveTCL installed. > install.package ...
written 8.2 years ago by Ying Chen110
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sva package for R 2.13.1?
... Hi guys, Is there anyone know where I can get the correct sva package for R2.13.1? I downloaded and installed the zipped sva package from author's website, but got error message when I tried to launch it. > utils:::menuInstallLocal() package 'sva' successfully unpacked and MD5 sums checked > ...
sva written 8.2 years ago by Ying Chen110 • updated 8.2 years ago by James W. MacDonald51k

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