User: Xinsen Xu

gravatar for Xinsen Xu
Xinsen Xu30
Reputation:
30
Status:
New User
Location:
US/Boston/Harvard
Last seen:
3 years, 6 months ago
Joined:
5 years, 2 months ago
Email:
x*******@gmail.com

Posts by Xinsen Xu

<prev • 11 results • page 1 of 2 • next >
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"inSilicoDB" package in R can't access to webservice
... Hi, everyone, I'm new to the inSilicoDB, and have a problem when I tried to use it. eset = getDataset("GSE4635", "GPL96") Error: Webservice not accessible. Please check your internet connection.: Error in function (type, msg, asError = TRUE) : Failed to connect to insilicodb.com port 443: Connectio ...
R written 3.6 years ago by Xinsen Xu30 • updated 3.6 years ago by sysbiocoder180
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MECDF (Multivariate Empirical Cumulative Distribution Functions)
... Hi guys,  I'm trying to use the "mecdf" package to analyze some data. After I used the below script or install the "mecdf_0.5.0.tar", when I entered "m = mecdf(x)", it turned out to be:   Error in extend(FUNCTION(.mecdf.main), "mecdf", continuous, Fh, Fst, nraw,  :  unused arguments (continuous, ...
R written 5.1 years ago by Xinsen Xu30
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Answer: A: How to deal with the CNV file and NOCNV file measured by Affy SNP6.0 of level 3
... Hi, this is really a nice topic. I'm also starting analyzing the cnv level-3 data. May I ask that how did you map the genes to the cnv.seg file? I've got this data, and I want to annotate the gene names to this file, so that I could know copy number changes of some important genes. I see that you m ...
written 5.1 years ago by Xinsen Xu30 • updated 7 months ago by RamRS28k
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TCGA/Broad Institute CNV Files Segment Annotation
... Hi guys, I try to use the TCGA copy number segment files to analyze the specific gene copy number change. I've downloaded the data, and it looked like this  Sample    Chromosome    Start    End    Num_Probes    Segment_Mean TCGA-3M-AB46-01A-11D-A40Z-01    1    3218610    9104465    3536    0.3108 ...
snp written 5.1 years ago by Xinsen Xu30 • updated 5.1 years ago by Na Sed300
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Comment: C: TCGA/Broad Institute CNV Files Segment Mean
... Thanks for the information. May I ask that why should we also "*2 (multiply by 2)" in the "(2^seg_mean)*2", instead of just "2^seg_mean"? Dose this "2" represent the normal intensity? ...
written 5.1 years ago by Xinsen Xu30
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Comment: C: How to select checkbox with specific names on web page (the TCGA data)
... Hi Karl, Thanks so much. I've downloaded the TCGA-Assembler, however, after I installed the Rtools31 and downloaded the httr version 0.5.0., and tried to type install.packages("httr_0.5.tar.gz", type="source", repos=NULL) it turned out that "ERROR: dependency 'jsonlite' is not available for packag ...
written 5.2 years ago by Xinsen Xu30
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How to select checkbox with specific names on web page (the TCGA data)
... Hi, I want to download the rna-seq data from the TCGA website. After I built the data matrix on the TCGA website, there are hundreds of the checkboxes. However, I only want to download the ones with the specific name "rsem.genes.normalized_results", because I only needed the normalized data. It is t ...
rna-seq written 5.2 years ago by Xinsen Xu30 • updated 5.2 years ago by karl.stamm3.7k
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Comment: C: What package to use in bioconductor to draw heatmap like this
... Thanks TriS. I found this ggplots tutorial might be useful. I'll try to run and have a look. http://stackoverflow.com/questions/5687891/r-how-do-i-display-clustered-matrix-heatmap-similar-color-patterns-are-grouped ...
written 5.2 years ago by Xinsen Xu30
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Comment: C: What package to use in bioconductor to draw heatmap like this
... So sorry that it's my first time to post here. I tried to upload an image of the heatmap, however failed.  Now I''ve added the link. Please check. Thanks. ...
written 5.2 years ago by Xinsen Xu30
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Comment: C: What package to use in bioconductor to draw heatmap like this
... Thank you so much Sean!  I wanna to cluster the cancer patients into 3 or 4 different groups, with obvious different overall survival of each group. I just try to imitate the nature paper as the link: http://www.nature.com/nature/journal/v497/n7447/fig_tab/nature12113_F3.html Ideally, i wanna the ...
written 5.2 years ago by Xinsen Xu30

Latest awards to Xinsen Xu

Popular Question 4.4 years ago, created a question with more than 1,000 views. For What package to use in bioconductor to draw heatmap like this
Popular Question 4.4 years ago, created a question with more than 1,000 views. For TCGA/Broad Institute CNV Files Segment Annotation
Student 5.2 years ago, asked a question with at least 3 up-votes. For What package to use in bioconductor to draw heatmap like this

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