User: nazaninhoseinkhan

Reputation:
340
Status:
Trusted
Location:
Iran, Islamic Republic Of
Last seen:
21 hours ago
Joined:
4 years, 10 months ago
Email:
n****************@gmail.com

I am Nazanin Hosseinkhan, PhD in Bioinformatics. My background is Microbiology and I am seeking for a postdoc position.

Posts by nazaninhoseinkhan

<prev • 241 results • page 1 of 25 • next >
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Comment: C: how to generate CNV plot from VEP results
... I have another question. This is the image of one of my stages: ![enter image description here][1] As you see I have some significant aberrations in chromosomes 7, 8, 12 and 16. However in the annotation file produced by biomaRt none of these have significant q-values. Moreover several other aber ...
written 5 days ago by nazaninhoseinkhan340
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Comment: C: how to generate CNV plot from VEP results
... Hi Kevin, I am suspected to my results. This is the header of the out put (GISTIC file) of GenomicRanges package: Type Chromosome Start End q-value G-score Del 1 61808 4364407 1 0 Del 1 4364472 4364634 0.49383 0 Del 1 4366964 5706597 1 0 Del 1 5707162 5707499 0.49383 0 Del 1 ...
written 5 days ago by nazaninhoseinkhan340
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Comment: C: Annotation of huge number of CNV files
... If I remember, there were 4 different files for each sample. normal hg19, tumor hg19, normal hg18 and tumor hg18. Depends on what reference genome version (hg18 or hg19) you want to use you can select them. ...
written 7 days ago by nazaninhoseinkhan340
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Comment: C: Annotation of huge number of CNV files
... I re-run my analysis on a cluster (server) and the problem was solved. ...
written 7 days ago by nazaninhoseinkhan340
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Comment: C: Annotation of huge number of CNV files
... Hi, I used the clinical data provided for my cancer of interest. I filter the clinical data for the specific stage and then use the TCGA codes for separating the original CNV files. ...
written 7 days ago by nazaninhoseinkhan340
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problem in interpretation of Gistic copy number analysis
... Dear all, I want to filter the final results of Gistic program. Strangely all aberrations have G-scores=0, however large number of aberrations have significant q-values (<0.15). I know that G-score reports the amplitude and the frequency of each aberrations across all samples. How can I int ...
gistic g-score copy number alteration written 7 days ago by nazaninhoseinkhan340
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Comment: C: how to generate CNV plot from VEP results
... Hi Kevin, I have 283 stage i, 50 stage ii, 111 stage iii and 54 stage iv. They are all mixed between normal and tumor. I want to find sequential changes occurred moving from stage i to stage iv. Is it biologically meaningful? I am asking this question because I expected to see changes in stage i ...
written 12 days ago by nazaninhoseinkhan340
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Comment: C: how to generate CNV plot from VEP results
... Yes Kevin, I saw the cnvplot in your paper. It is so dense. however my cnvplots are so sparse(with only few peaks). If you remember I am working on different stages of cancer (stage i-iv). Can I send you the input data of one stage (stage i) to repeat the analysis? Before reporting the results I wa ...
written 13 days ago by nazaninhoseinkhan340
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Comment: C: how to generate CNV plot from VEP results
... I see this figure in this paper: "Comprehensive molecular portrait using next generation sequencing of resected intestinal-type gastric cancer patients dichotomized according to prognosis". I tried Gistic 2.0 on GenePattern too. However strangely I got no genes, means no one has the qvalue lower t ...
written 13 days ago by nazaninhoseinkhan340
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Comment: C: how to generate CNV plot from VEP results
... Sorry, the following is the plot I meant: ![CNV plot with gene names][1] [1]: https://image.ibb.co/bLQ4pU/plot.jpg ...
written 13 days ago by nazaninhoseinkhan340

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