User: lhaiyan3

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lhaiyan310
Reputation:
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New User
Location:
United States
Last seen:
1 month, 2 weeks ago
Joined:
2 years, 3 months ago
Email:
l*******@gmail.com

Posts by lhaiyan3

<prev • 27 results • page 1 of 3 • next >
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Comment: C: How to use GSVA for the RNA-seq RPKM file
... Hi, Kevin: Thanks so much for your quick reply. I got the heatmap fig according to your script. I will following your suggestions to set up the different sub-group. You really help me a lot! best HY ...
written 7 weeks ago by lhaiyan310
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Comment: C: How to use GSVA for the RNA-seq RPKM file
... Hi, Kevin: Thanks so much for your script. I followed your biomaRt script and now I can get the gsva enrichment score. Sorry I still have another question about how to get the heatmap. Your protocol is about the disease vs control sample comparison. We just have 16 samples in the dataset, no compar ...
written 7 weeks ago by lhaiyan310 • updated 7 weeks ago by Kevin Blighe13k
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Comment: C: How to use GSVA for the RNA-seq RPKM file
... Hi, Kevin: Thanks very much for your quick reply. I followed your suggestions and got the following wrong message again, can you please help me check? > gsva.scores <- gsva(data.matrix(RPKM), gene.sets, method="gsva", mx.diff=TRUE, verbose=TRUE, rnaseq=TRUE, parallel.sz=8) Error in .local(ex ...
written 8 weeks ago by lhaiyan310
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How to use GSVA for the RNA-seq RPKM file
... Dear all, I am trying to use GSVA for the RNA-seq analysis. I have the refseq annotation based RPKM files for the RNA-seq. RPKM <- read.table("test.txt",header=TRUE,row.names=1,sep="\t") #C2 collection of curated gene sets that form part of the Molecular Signatures Database (MSigDB) ver ...
rna-seq written 8 weeks ago by lhaiyan310 • updated 8 weeks ago by Kevin Blighe13k
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Comment: C: GSVA on RNAseq data
... Hi, colonppg: Can you use GSVA for your RNA-seq RPKM data now? Can you please share your R script with me? I still have a lot problem with it. Thanks very much. HY ...
written 9 weeks ago by lhaiyan310
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how to use ESTIMATE to infer tumor purity and stromal score from RNA-seq data?
... Dear all: Did anyone use ESTIMATE (http://bioinformatics.mdanderson.org/main/ESTIMATE:Overview) to infer tumor purity and stromal score from RNA-seq before? I am not clear how to use this tool and what is the input file format for this tool? They are just several steps, and i did not figure out ho ...
rna-seq written 4 months ago by lhaiyan310
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how to extract the RD, AD, VAF information for the normal and tumor samples from the MuTect2 output vcf file?
... Dear all: I have the tumor-normal pair Mutect2 output VCF file. I want to get the DP, RD, AD and VAF information for both tumor and normal samples. Can anyone please give me some suggestions? Thanks very much. best HY ...
exom-seq mutect2 written 6 months ago by lhaiyan310 • updated 6 months ago by Biostar ♦♦ 20
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Comment: C: comparing single cell RNA-seq and bulk RNA-seq results
... Hi, Did you find the good way to do this? Thanks. HY ...
written 6 months ago by lhaiyan310
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Comment: C: Best way to present the single cell RNA-seq data and bulk RNA-seq expression dat
... Hi, Did you find the good way to do this? Thanks. HY ...
written 6 months ago by lhaiyan310
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Comment: C: How to analyze the targeted RNA-panel data?
... Hi, vchris: Thanks for your great suggestions for me. Sorry I still need your help. Our data is the customerized Qiagen targeted RNAscan panel data. I contacted with the CLC technical support, the CLC biomedical workbench currently did not have the plug in for this kind of analysis. I need to use t ...
written 7 months ago by lhaiyan310

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