User: Cheng-Yuan Kao

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Posts by Cheng-Yuan Kao

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Answer: A: DESeq2 installation error
... Hi,  I tried this (Bioconductor version 3.5 (BiocInstaller 1.26.1)). > install.packages("RcppArmadillo")  And I keep getting this error:  ld: warning: directory not found for option '-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0' ld: warning: directory not found for option '-L/usr ...
written 10 days ago by Cheng-Yuan Kao80
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change the biomaRt host
... Hi, there, I was able to use biomaRt before but I just got error message when I did : > ensembl = useMart("ensembl") Space required after the Public Identifier SystemLiteral " or ' expected SYSTEM or PUBLIC, the URI is missing Opening and ending tag mismatch: hr line 7 and body Opening and end ...
biomart written 23 months ago by Cheng-Yuan Kao80 • updated 23 months ago by hygine140
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Answer: A: Questions regarding convertIDs in the rnaseqGene Package
... Great. Thanks for your help.  I followed your suggestion and did: > deg_01$newMGI_symbol <- convertIDs(as.character(deg_01$id), "REFSEQ", "SYMBOL", org.Mm.eg.db) It worked. I did not know that factor vs character makes such a difference because the same input works well with biomaRt . ...
written 2.5 years ago by Cheng-Yuan Kao80
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Questions regarding convertIDs in the rnaseqGene Package
... Hey, there, I was following the instruction of http://www.bioconductor.org/help/workflows/rnaseqGene/#annotate to update the annotation in my DEG files.  I used the code they designed:  convertIDs <- function( ids, from, to, db, ifMultiple=c("putNA", "useFirst")) { stopifnot( inherits( db, " ...
rnaseqgene convertids written 2.6 years ago by Cheng-Yuan Kao80
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Comment: C: multi genome comparison
... Yes. That was my original thought too. I was wondering whether there is a more straight forward method. On Wed, Feb 24, 2010 at 12:41 PM, Michael Lawrence < lawrence.michael@gene.com> wrote: > > > On Wed, Feb 24, 2010 at 9:41 AM, Cheng-Yuan Kao wrote: > >> I did check inpa ...
written 7.7 years ago by Cheng-Yuan Kao80
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Comment: C: multi genome comparison
... I did check inparanoid before. My impression is that inparanoid only does two species comparison although they seem to have all the species we need. Any thoughts? On Wed, Feb 24, 2010 at 9:36 AM, Michael Lawrence wrote: > Take a look at the inparanoid annotation packages. May or may not have a ...
written 7.7 years ago by Cheng-Yuan Kao80
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multi genome comparison
... Hi, there, We are trying to identify genes conserved in 5 eukaryotic species but not in 3 other eukaryotic species. Is there a way to do it with some websites? Or is there a program from somewhere or a package from Bioconductor tailored for this? Your suggestions will be appreciated. [[ ...
written 7.7 years ago by Cheng-Yuan Kao80 • updated 7.7 years ago by Michael Lawrence9.6k
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Comment: C: Is there a package or a way to convert "probesets" to "genes"
... Thanks a lot. It is very helpful and I will look into the help pages as well. I am wondering how many "gene-based summary" in articles I read are actually "transcript-based summary". Most of these papers report differentially expressed "genes". When I met the first authors and asked them the questi ...
written 7.9 years ago by Cheng-Yuan Kao80
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Comment: C: Is there a package or a way to convert "probesets" to "genes"
... Hi, We have C. elegans expression data set. Do you know what exactly [!is.na(entrezIDs) & !duplicated(entrezIDs)] does? Thanks. Cheng-Yuan On Tue, Nov 17, 2009 at 3:34 AM, Yuan Hao wrote: > Hi Richie, > > I am not sure which data set and annotation package you are working on, > ...
written 7.9 years ago by Cheng-Yuan Kao80
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Is there a package or a way to convert "probesets" to "genes"
... Hi, there, I have a question regarding Affy chip data. We did many expression arrays and used LIMMA to get the differentially expressed "genes" (control vs treatment). However I found that some probesets have multiple genes according to Affy annotation file. On the other hand, multiple probeset ...
microarray affy limma convert written 7.9 years ago by Cheng-Yuan Kao80 • updated 7.9 years ago by Tobias Straub410

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Popular Question 23 months ago, created a question with more than 1,000 views. For change the biomaRt host

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