User: ycding

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ycding10
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10
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New User
Location:
United States
Last seen:
2 years, 6 months ago
Joined:
2 years, 8 months ago
Email:
y*****@coh.org

Posts by ycding

<prev • 6 results • page 1 of 1 • next >
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Answer: A: CPM output from edgeR for a downstream application
... Hi Aaron, thank you so much for your quick answer!!   I am going to use the integrative analysis method developed by Dr. Iterson etal published in Nuclear Acid Research( integerative analysis of microarray and mRNA expression);  yes, the integrative idea is similar to what you suggested, first use ...
written 2.5 years ago by ycding10
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CPM output from edgeR for a downstream application
... Dear edgeR users, I am not an experienced R user.  I ran the edgeR for the TCGA RNAseq  data using raw count from the Rsubread featureCounts  and the TCGA miRNAseq data using raw count from TCGA level3 data to identify differential expressed genes, see the codes below;  now I want to examine miRNA ...
edger cpm written 2.5 years ago by ycding10
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Comment: C: how to analyze TCGA CNV data
... Hi Martin, I downloaded from TCGA website,  freely publicly available for level3 data. https://tcga-data.nci.nih.gov/tcga/dataAccessDownload.htm ...
written 2.6 years ago by ycding10
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how to analyze TCGA CNV data
... Dear R people, I downloaded TCGA CNV data in the following format;  I am not familiar with CNV data and  want to know how to process and analyze this type of data, for example, how to convert segment mean to copy number,  how to add gene IDs for each chromosome region. I have RNA seq data for the s ...
tcga cnv correlation between mrna exprssion and cnv written 2.7 years ago by ycding10 • updated 21 months ago by spulido990
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Answer: A: Can I feed TCGA normalized count data to EdgeR for differential gene expression
... Hi Stephen and Aaron, thank you so much for your quick help.  I briefly checked into the link provided by Stephen, it is a very good data source,  I will definitely look into it.  ...
written 2.7 years ago by ycding10
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Can I feed TCGA normalized count data to EdgeR for differential gene expression analysis
... Dear R people, I downloaded TCGA level3 RNAseq data for 63 prostate tumor samples with conditions (age difference) I am interested in. I want to identify differential expressed genes between two age groups. I am reading the user guide for the EdgeR program and found that it takes integer count data ...
edger tcga normalized count written 2.7 years ago by ycding10 • updated 2.7 years ago by alakatos80

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