User: lovetl2002

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lovetl200240
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Posts by lovetl2002

<prev • 7 results • page 1 of 1 • next >
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Meaning of abbreviations of last-follow-up status in the 2000 breast cancer dataset?
... I'm currently working on the 2000 breast cancer dataset: http://www.nature.com/nature/journal/v486/n7403/full/nature10983.html   There is a last_follow_up_status column in the phenotype data. The four levels of this factor are: a d d-d.s. d-o.c. null Since I cannot find out any description of ...
breast cancer cancer written 3.8 years ago by lovetl200240
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illumina beadarray expresion matrix transformation problem
... This is my first time dealing with beadarray data. For Affymetrix microarray data, I can easily log-transform it. However for beadarray data, after log-transformation, the shape of the data didn't change too much. For one single sample, after log transformation:   So how can I transform the da ...
R gene expression beadarray microarray written 3.8 years ago by lovetl200240 • updated 3.8 years ago by Ying W3.9k
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Comment: C: How to extract protein interactions from a reactome biopax file?
... Thank you. The problem is that I'm not familiar with Java. I'm familiar with R and Python though. ...
written 4.3 years ago by lovetl200240
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Homologous gene matching between mouse and human
... There is a small part of mouse genes that cannot be matched to homologous human genes. For example, the Apoc1 gene: http://www.informatics.jax.org/marker/MGI:88053   Since there is a gene, APOC1, with exactly the same symbol in human, why is this mouse Apoc1 gene not homologous to human APOC1 gen ...
gene hgnc mgi written 4.3 years ago by lovetl200240 • updated 4.3 years ago by Jean-Karim Heriche18k
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How to extract protein interactions from a reactome biopax file?
... Hello, I'm currently working with Reactome database.  I want to get the protein interaction pairs of mouse. However, the file Reactome provided for download is not up to date. A lot of the pairs showed in the browser are missing. So I decide to extract these pairs from the BioPax file they provided ...
network reactome biopax written 4.3 years ago by lovetl200240 • updated 4.3 years ago by rodche60
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Comment: C: How to determine whether a gene is present or absent?
... Thanks. What if I use microarray data? ...
written 4.5 years ago by lovetl200240
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How to determine whether a gene is present or absent?
... Suppose I have a level-3 expression matrix from TCGA (normalized), how to filter out absent genes before further processing like gene coexpression analysis?  Currently what I do is:   1. Set a lower threshold, like 5% quantile of all the expression level. 2. Test whether a gene have enough portio ...
tcga microarray rna-seq written 4.5 years ago by lovetl200240 • updated 3.3 years ago by fatima0

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Popular Question 3.8 years ago, created a question with more than 1,000 views. For How to determine whether a gene is present or absent?

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