User: Xianjun

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Xianjun190
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Great Boston Area
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http://sterding.com/
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a genome reader

Posts by Xianjun

<prev • 23 results • page 1 of 3 • next >
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Answer: A: heatmap.2 reorder branches
... I had the same problem of using the order function with proper weight, and I just figured out the trick. Taking the `mtcars` dataset in e.rempel's example above, we first run the default `hclust` to get the dendrogram. data(mtcars) x <- as.matrix(head(mtcars)) # only using the first 6 ...
written 11 weeks ago by Xianjun190
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Answer: A: Illumina'S Genome Studio Final Report: Forward Or Top Allele?
... For those who are still not clear with the difference columns in the FinalReport.txt (from GenomeStudio), e.g. Allele1 - Forward, Allele2 - Forward, Allele1 - Top, Allele2 - Top, Allele1 - Plus, Allele2 - Plus, a short answer is: TOP/BOT is for Illumina's own strand designations (which is pretty sma ...
written 11 months ago by Xianjun190
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Comment: C: How to correctly use the color option in R image() function?
... Thanks for your comments, Deepak.  As my reply below, I guess I figured it out: We always get min(x)=col[1], max(x)=col[last]. For your case, then there are 6 colors, again, 1=blue, 3=grey, 2=green (since it's left close). ...
written 2.4 years ago by Xianjun190
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Answer: A: How to correctly use the color option in R image() function?
... OK I figured it out myself:  Unless the breaks is set, the range of Z (or x in above example) is evenly cut into N intervals (where N = the length of color) and values in Z are proportionally assigned to the nearest color. For example, when x=c(3,1,2,1) and col=c("blue","red",'green','yellow'), th ...
written 2.4 years ago by Xianjun190
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How to correctly use the color option in R image() function?
... HI, I got a question about how to assign color value in image() function. I thought the col option works as a vector with the same length of Z, with color of each cell in the matrix Z corresponding to the values in. However, it confused me with different result. To make my question simple, let's s ...
image R written 2.4 years ago by Xianjun190
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Answer: A: Bed File With Introns Only
... Here is an easy example code to convert bed12 --> intron, 5' UTR, 3' UTR, CDS etc.  http://onetipperday.blogspot.com/2012/11/get-intron-utr-cds-from-bed12-format.html If you want to get meta-intron (i.e. merge overlapped introns from one gene into one intron), you can use the code snip below: ...
written 2.4 years ago by Xianjun190
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Are the rlog or VST values from DESeq2 comparable across genes?
... Dear DESeq2 community, I know I can use the rlog or VST (variance stabilized transformed) value from DESeq2 for sample clustering and visualization. I am wondering what else I can use it for. Can I use it as normalized expression value to compare expression between different genes, e.g. cluster gen ...
deseq2 written 2.5 years ago by Xianjun190
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Comment: C: Why Are There Many Rna-Seq Hits To Intronic Regions?
... Hi Heng, did you get any idea how to check whether DNA/pre-mRNA contamination or nascent RNAs lead the intergenic mapped reads? I am facing the same problem to explain the non-exonic mapper. Thanks. ...
written 2.6 years ago by Xianjun190
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Answer: A: How To Generate Random Size Matched Background Regions
... Here is a simply script I wrote for this purpose, using bedtools random and a input.bed as background.  # =============================================================== # Script to generate a random size-matched background regions # Author: Xianjun # Date: Jun 3, 2014 # Usage: # toGenerateRandomR ...
written 3.0 years ago by Xianjun190
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Comment: C: cufflinks output file isoforms.fpkm_tracking has mixed ENSGxxx and ENSTxxx ID in
... Thank you for your reply, Bert.  You are right; the GTF file does contain both gene and transcript, they are organized in a hierarchical way (e.g. gene --> transcripts --> exons).  But given the fact that cufflinks outputs both Transcript-level expression and Gene-level expression separately ...
written 3.2 years ago by Xianjun190

Latest awards to Xianjun

Great Question 6 months ago, created a question with more than 5,000 views. For Any Quick Sort Method For Large Bed File As 20G In Size?
Popular Question 21 months ago, created a question with more than 1,000 views. For Computational Biologist In Brain Research, Harvard Medical School, Boston, Us
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Computational Biologist In Brain Research, Harvard Medical School, Boston, Us
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: How to correctly use the color option in R image() function?
Scholar 2.4 years ago, created an answer that has been accepted. For A: How to correctly use the color option in R image() function?
Student 2.4 years ago, asked a question with at least 3 up-votes. For Why Does Cufflinks With Mask (-M) Option Have Lower Fpkm For Mrna Genes?
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Any Quick Sort Method For Large Bed File As 20G In Size?
Supporter 3.0 years ago, voted at least 25 times.
Appreciated 3.3 years ago, created a post with more than 5 votes. For Any Quick Sort Method For Large Bed File As 20G In Size?
Popular Question 3.5 years ago, created a question with more than 1,000 views. For Any Quick Sort Method For Large Bed File As 20G In Size?
Student 3.9 years ago, asked a question with at least 3 up-votes. For Why Does Cufflinks With Mask (-M) Option Have Lower Fpkm For Mrna Genes?
Student 4.5 years ago, asked a question with at least 3 up-votes. For Any Quick Sort Method For Large Bed File As 20G In Size?

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