User: tangming2005

gravatar for tangming2005
tangming200590
Reputation:
90
Status:
Trusted
Location:
United States
Last seen:
3 weeks, 1 day ago
Joined:
3 years, 3 months ago
Email:
t***********@gmail.com

Posts by tangming2005

<prev • 112 results • page 1 of 12 • next >
0
votes
1
answers
79
views
1
answers
Comment: C: claariom.s.human annotation error
... Thanks James. I upgraded R to the current. and somehow the old bioc packages are still linked to the new R version... The other way indeed worked. Best, Ming ...
written 4 weeks ago by tangming200590
2
votes
1
answer
79
views
1
answer
claariom.s.human annotation error
... code are below. Thank you! library(limma) library(oligo) library(pd.clariom.s.human) celFiles <- list.celfiles('.', full.names=TRUE) ab<- read.celfiles(celFiles) eset<- oligo::rma(ab) library("affycoretools") eset <- annotateEset(eset, annotation(eset)) Error: There appears to be ...
affcoretools pd.clariom.s.human written 4 weeks ago by tangming200590 • updated 4 weeks ago by James W. MacDonald45k
0
votes
2
answers
113
views
2
answers
Comment: C: unlist a exons GRangeslist object and add a gene name column
... good to know this! thanks. ...
written 5 weeks ago by tangming200590
0
votes
2
answers
113
views
2
answers
Comment: C: unlist a exons GRangeslist object and add a gene name column
... Thanks! How can I miss this function?!    If it is a list (not GRangesList) object, I would do  myname<- names(mylist) lapply(myname, function(x) mylist[[x]]$gene<- x) stack is very useful!   ...
written 5 weeks ago by tangming200590
5
votes
2
answers
113
views
2
answers
unlist a exons GRangeslist object and add a gene name column
... Hi, I can not find  a way to do it. exons <- exonsBy(TxDb.Hsapiens.UCSC.hg19.knownGene, by = "gene") unlist(exons) # this will lost the gene name information. How do I add the name of the gene for the exons? I have read https://www.biostars.org/p/101513/ and https://support.bioconductor.or ...
granges grangeslist txdb.hsapiens.ucsc.hg19.knowngene written 5 weeks ago by tangming200590 • updated 5 weeks ago by Hervé Pagès ♦♦ 13k
0
votes
1
answers
282
views
1
answers
Comment: C: POU5F1(OCT4) /ENTREZID: 5460 is not in the TxDb.Hsapiens.UCSC.hg19.knownGene
... Hi James, thanks very much for this detailed answer. now I remember a related question you answered me some time ago https://support.bioconductor.org/p/88725/#88767 again, your help is much appreciated. learned a lot! Tommy ...
written 11 weeks ago by tangming200590
0
votes
1
answers
282
views
1
answers
Comment: C: POU5F1(OCT4) /ENTREZID: 5460 is not in the TxDb.Hsapiens.UCSC.hg19.knownGene
... thanks. looks like I can not find DAXX, HLA-A, SHOX and TRIM27 in TxDb.Hsapiens.UCSC.hg19.knownGene even using the other names. but POU5F1B is not shown either AnnotationDbi::select(org.Hs.eg.db, c("POU5F1", "DAXX", "HLA-A","SHOX","TRIM27"), keytype = "SYMBOL", columns = "ALIAS") 'select()' ret ...
written 11 weeks ago by tangming200590
0
votes
1
answers
282
views
1
answers
Comment: C: POU5F1(OCT4) /ENTREZID: 5460 is not in the TxDb.Hsapiens.UCSC.hg19.knownGene
... Thanks! I have a list of genes which I can not find in the txdb. DAXX, HLA-A, SHOX and TRIM27. where can I find the alternative names? Tommy   ...
written 11 weeks ago by tangming200590
2
votes
1
answer
282
views
1
answer
POU5F1(OCT4) /ENTREZID: 5460 is not in the TxDb.Hsapiens.UCSC.hg19.knownGene
... Hi, I was trying to get the coordinates of some genes, and was surprised that POU5F1 gene is not in the txdb. Thank you for looking into this. Tommy library(TxDb.Hsapiens.UCSC.hg19.knownGene) txdb<- TxDb.Hsapiens.UCSC.hg19.knownGene hg19.genes<- genes(txdb) library(AnnotationDbi) libra ...
txdb.hsapiens.ucsc.hg19.knowngene written 12 weeks ago by tangming200590 • updated 11 weeks ago by jma199130
0
votes
1
answers
538
views
1
answers
Comment: C: reads2pairs from TEQC error:Error in reads2pairs(reads) : read pair IDs do not s
... samtools view -F 256 will remove some reads, but not all not uniquely mapped reads. Have you tried TEQC on any BWA-MEM aligned bam files? from Heng Li: https://www.biostars.org/p/59281/#59303 Eland is probably the first short read aligner. It reports a tag, which can be '[UR][0-2]|NM', for each r ...
written 4 months ago by tangming200590

Latest awards to tangming2005

Popular Question 20 months ago, created a question with more than 1,000 views. For DESeq2 for ChIP-seq differential peaks
Popular Question 20 months ago, created a question with more than 1,000 views. For annotate GRanges with upstream or downstream nearest gene
Supporter 20 months ago, voted at least 25 times.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 164 users visited in the last hour