User: Irsan

gravatar for Irsan
Irsan6.8k
Reputation:
6,780
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Location:
Amsterdam
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Last seen:
2 days, 12 hours ago
Joined:
6 years, 2 months ago
Email:
i**********@gmail.com

PhD-student at Clinical Genetics, VU medical centre

Posts by Irsan

<prev • 496 results • page 1 of 50 • next >
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Comment: C: Workshop: Data manipulation and visualization with Python (3 places left)
... From now, 2 places left! Just signed up for the course. Looks promising! ...
written 22 months ago by Irsan6.8k
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Comment: C: Fastq Convert To Fasta
... OK, I have changed fasta to fastq ...
written 2.1 years ago by Irsan6.8k
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Answer: A: Heatmap trouble in R
... Because it scales the data. Use the scale="none" option ...
written 2.2 years ago by Irsan6.8k
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Comment: C: Is microarray gene expression analysis is dead ?
... Oh yeah that's right, forgot about that... ...
written 2.2 years ago by Irsan6.8k
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Comment: C: How to draw lego plot Using Mutation Data (MAF format input)?
... I would advice against it. Becuase of the three dimensions, some bars can block others. ...
written 2.2 years ago by Irsan6.8k
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Answer: A: Is microarray gene expression analysis is dead ?
... In research, micro-arrays are on their return but in clinical diagnostics they are still used a lot, in particular array-CGH or SNP-arrays to determine germ line CNVs that predispose to disease. ...
written 2.2 years ago by Irsan6.8k
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Comment: C: Calculate LogR ratio and BAF from X and Y intensities
... A sample for which you now the ploidy = 2. So any non-cancer sample would be fine. I think most of the time in a SNP-array run such a sample is included, for example a male and female reference DNA sample. It depends all on your research context but most of the time, best scenario is when you have a ...
written 2.4 years ago by Irsan6.8k
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Answer: A: Calculate LogR ratio and BAF from X and Y intensities
... BAF = Y / (X + Y) LRR = log2( (X + Y)sampleOfInterest / (X+Y)baselineSample) But you might want to do some normalization first, possbily with beadstudio or with tQn normalization. See here http://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-9-409 ...
written 2.4 years ago by Irsan6.8k
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Comment: C: How to get counts of STAR output (sam/bam).
... Hmm I still use star + htseq. I need to update my star version ...
written 2.5 years ago by Irsan6.8k
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Answer: A: How to get counts of STAR output (sam/bam).
... [HTseq][1] is another popular option [1]: http://www-huber.embl.de/HTSeq/doc/overview.html ...
written 2.5 years ago by Irsan6.8k

Latest awards to Irsan

Good Answer 10 months ago, created an answer that was upvoted at least 5 times. For A: If you have a chance to ask questions to the CEO of Illumina, what would you do?
Good Answer 10 months ago, created an answer that was upvoted at least 5 times. For A: Random Genomic Regions Of A Given Length Distribution
Scholar 10 months ago, created an answer that has been accepted. For A: Bedtools Genomecoveragebed Usage : How To do per base coverage analysis for only
Popular Question 11 months ago, created a question with more than 1,000 views. For Fastq Format Redundancy
Popular Question 11 months ago, created a question with more than 1,000 views. For Cancer genomics journals
Good Answer 15 months ago, created an answer that was upvoted at least 5 times. For A: If you have a chance to ask questions to the CEO of Illumina, what would you do?
Appreciated 15 months ago, created a post with more than 5 votes. For C: Superimpose 2 Heatmaps
Appreciated 15 months ago, created a post with more than 5 votes. For C: Conditional Coloring Of Heatmaps
Popular Question 15 months ago, created a question with more than 1,000 views. For Revolution (?) in CNA detection using exome/targeted sequencing
Popular Question 15 months ago, created a question with more than 1,000 views. For Fastq Format Redundancy
Appreciated 16 months ago, created a post with more than 5 votes. For C: Superimpose 2 Heatmaps
Great Question 16 months ago, created a question with more than 5,000 views. For Why Is Stranded Rna Seq Better Than Unstranded?
Popular Question 18 months ago, created a question with more than 1,000 views. For Does Bedops Have A Command Similar To The Bedtools Makewindows?
Popular Question 18 months ago, created a question with more than 1,000 views. For Revolution (?) in CNA detection using exome/targeted sequencing
Good Answer 20 months ago, created an answer that was upvoted at least 5 times. For A: Coverage Calculation
Epic Question 22 months ago, created a question with more than 10,000 views. For Why Is Stranded Rna Seq Better Than Unstranded?
Popular Question 23 months ago, created a question with more than 1,000 views. For Monitor Hiseq Run Remotely Linux
Teacher 2.0 years ago, created an answer with at least 3 up-votes. For A: Titv Meaning
Epic Question 2.2 years ago, created a question with more than 10,000 views. For Why Is Stranded Rna Seq Better Than Unstranded?
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Mysql-Query On Go-Database Ucsc Server
Commentator 2.4 years ago, created a comment with at least 3 up-votes. For C: What Is The Difference Between Structural Variants (Svs) And Copy-Number Variant
Good Answer 2.5 years ago, created an answer that was upvoted at least 5 times. For A: Coverage Calculation
Appreciated 2.5 years ago, created a post with more than 5 votes. For C: Superimpose 2 Heatmaps
Appreciated 2.6 years ago, created a post with more than 5 votes. For C: Superimpose 2 Heatmaps

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