User: Jan Oosting

gravatar for Jan Oosting
Jan Oosting920
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920
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Trusted
Location:
Leiden, NL
Last seen:
6 months, 1 week ago
Joined:
10 years, 10 months ago
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j**********@gmail.com

Posts by Jan Oosting

<prev • 32 results • page 1 of 4 • next >
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Comment: C: Pathways Analysis in R
... You can use your own signatures with these types of tests, because they're basically repeated chi-square, or Fisher exact tests, where you test whether the proportion of DEG is different between the population and your signature. i.e You test 20000 genes of which 200 ( 1%) are DE, your signatures co ...
written 6 months ago by Jan Oosting920
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Comment: C: Pathways Analysis in R
... You could use the globaltest bioconductor package ...
written 6 months ago by Jan Oosting920
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Comment: C: What should I do when some probes of a gene is detected as hypomethylated and ot
... You should probably look at the functional domains at which the probes are located. Pretty much all probes that are not close to the promoter region of a gene are usually methylated. I find it helps to visualize the location, and extent of methylation relative to the exons (and especially the first ...
written 12 months ago by Jan Oosting920
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Answer: A: What does mean when people say AAB copy-number state?
... The number of As and Bs stand for the number of alleles from each parent. Normal cells have one allele of each autosome from each parent, so the chromosomes 1-22, and all locations on those chromosomes are all AB. Normally you don't know which allele came from the mother and which allele came from ...
written 12 months ago by Jan Oosting920
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Comment: C: Hierarchical Clustering of copy number variations
... CNA from RNA data has been done in the past, but is very challenging You could use impute() to cover up NAs. but that will not help with entire rows of NAs ...
written 2.8 years ago by Jan Oosting920
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Answer: A: Why GC-content normalization for CNV analysis?
... There are both technical and biological reasons to do GC-content normalization. Technically, both PCR efficiency of target sequences, and binding of probes to target sequences are related to GC content of the sequence. Especially without normal samples this is a problem. The technical issues could ...
written 3.2 years ago by Jan Oosting920
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Answer: A: A simple question about Affymetrix SNP platform
... For each of the types (PMA, MMA, PMB, MMB) there are upto 10 probes. (hence the 24-40 distinct probes earlier in the paragraph) The earlier SNP arrays also had shifting positions around the SNP if p is the basepair position of the SNP, then there were probes between p-12 and p+12, but also p-11 to p ...
written 4.7 years ago by Jan Oosting920
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Answer: A: Software for SNP zygosity and loss of heterozygosity
... You can have a look at the bioconductor quantsmooth package. It has plots to show chromosome bands together with your own data. ...
written 4.8 years ago by Jan Oosting920
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Answer: A: Illumina SNParray reading with beadarraySNP Bioconductor package
... You really should read the error message that is displayed when you run read.SnpSetIllumina() It informs you which fields are missing from the reportfile. Manifest files are not integrated into the result object. Only the data available in the reporrtfile. If you don't need the copy-number functi ...
written 4.8 years ago by Jan Oosting920
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Comment: A: How to get SNP 6.0 array data in R?
... You could use the crlmm Bioconductor package ...
written 5.0 years ago by Jan Oosting920

Latest awards to Jan Oosting

Guru 12 months ago, received more than 100 upvotes.
Good Answer 2.8 years ago, created an answer that was upvoted at least 5 times. For A: Drawing Chromosome Ideogams With Data
Scholar 4.6 years ago, created an answer that has been accepted. For A: A simple question about Affymetrix SNP platform
Teacher 4.6 years ago, created an answer with at least 3 up-votes. For A: Design Matrix For Pre-Subtracted Arrays
Teacher 5.3 years ago, created an answer with at least 3 up-votes. For A: Design Matrix For Pre-Subtracted Arrays
Appreciated 6.6 years ago, created a post with more than 5 votes. For A: Top/Bottom Confusion For Illumina Snp Calls
Appreciated 7.5 years ago, created a post with more than 5 votes. For A: Drawing Chromosome Ideogams With Data
Good Answer 7.5 years ago, created an answer that was upvoted at least 5 times. For A: Drawing Chromosome Ideogams With Data
Teacher 7.5 years ago, created an answer with at least 3 up-votes. For A: Design Matrix For Pre-Subtracted Arrays
Teacher 7.5 years ago, created an answer with at least 3 up-votes. For A: Exome Sequencing: Masking The Non-Genic Sequences ?
Teacher 7.5 years ago, created an answer with at least 3 up-votes. For A: Bioconductor Quantsmooth Sex Chromosome Error
Teacher 7.5 years ago, created an answer with at least 3 up-votes. For A: Reading Genotyping Data From Illumina Genomestudio Into R
Teacher 7.5 years ago, created an answer with at least 3 up-votes. For A: Set Local Bioconductor Repository
Teacher 7.5 years ago, created an answer with at least 3 up-votes. For A: What Is Your Favorite Visualizer For Acgh Or Snp Microarray Data?
Teacher 7.5 years ago, created an answer with at least 3 up-votes. For A: Top/Bottom Confusion For Illumina Snp Calls
Teacher 7.5 years ago, created an answer with at least 3 up-votes. For A: Drawing Chromosome Ideogams With Data

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