User: array chip

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array chip350
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Posts by array chip

<prev • 46 results • page 1 of 5 • next >
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Answer: A: biomaRt getBM error
... Thanks Mike. Yes it worked with your code! ...
written 13 months ago by array chip350
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biomaRt getBM error
... Hi, I am getting this error today. It worked just last week. can anyone suggest what's going on? > library(biomaRt) > ensembl=useMart("ensembl") > ensembl = useDataset("hsapiens_gene_ensembl",mart=ensembl) > getBM(attributes=c('hgnc_symbol', 'ensembl_gene_id', 'entrezgene','descriptio ...
biomart written 13 months ago by array chip350
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Comment: C: DESeq2 vs TCGAbiolinks normalization methods
... Thank you again! ...
written 15 months ago by array chip350
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Comment: A: DESeq2 vs TCGAbiolinks normalization methods
... Thank you Michael for your comments! If I start with raw counts, do your comments suggest I should run EDASeq's normalization first before using rlog() or vst() from DESeq2? Thanks again! ...
written 15 months ago by array chip350
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DESeq2 vs TCGAbiolinks normalization methods
... Hi all, I am still new to RNA-seq analysis. I understand DESeq2 offer rlog() and vst() as a normalization method to raw count data before running downstream analysis. I just came across TCGAbiolinks package for accessing the TCGA datasets. This package also offer its own normalization methods. Here ...
rnaseq normalization deseq2 written 15 months ago by array chip350
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Answer: A: SAMseq error message
... Thank you James. Unfortunately, I am trying to use survival analysis with RNA-seq data. Michael Love previously (in my another thread earlier) has suggested to use SAMseq for that purpose, because DESeq2 and edgeR do not work for survival models (wish this functionality can be added in the future). ...
written 18 months ago by array chip350
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Comment: C: SAMseq error message
... someone suggest this question is better answered on bioconductor, instead of in R community. so here is more info from what I have been trying: I did not do any pre-processing (normalization/transformation) and used raw counts in the SAMseq(). I tried to reduce the size of input data. I found out t ...
written 18 months ago by array chip350
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Comment: C: SAMseq error message
... sorry that I realized that samr package is in the R community, instead of bioconductor, so I posted it there again. Sorry if this annoys anyone. But would really appreciate if anyone responds if knowing what's going on with the error. ...
written 18 months ago by array chip350
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Comment: C: SAMseq error message
... Here is the info from  > biocValid() [1] TRUE > sessionInfo() R version 3.3.2 (2016-10-31) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 7 x64 (build 7601) Service Pack 1 locale: [1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETAR ...
written 18 months ago by array chip350
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SAMseq error message
... Hi, I am trying to using SAMseq() to analyze my RNA-seq experiment (20000 genes x 550 samples) with survival endpoint. It quickly give the following error: > library(samr) Loading required package: impute Loading required package: matrixStats Attaching package: ‘matrixStats’ The following obje ...
samseq written 18 months ago by array chip350

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Popular Question 5.4 years ago, created a question with more than 1,000 views. For CEL files not valid?
Popular Question 5.4 years ago, created a question with more than 1,000 views. For CEL files not valid?

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