User: nazaninhoseinkhan

Reputation:
410
Status:
Trusted
Location:
Iran, Islamic Republic Of
Last seen:
2 weeks, 3 days ago
Joined:
6 years, 11 months ago
Email:
n****************@gmail.com

I am Nazanin Hosseinkhan, PhD in Bioinformatics. My background is Microbiology and I am a researcher at Iran University of Medical Sciences.

Posts by nazaninhoseinkhan

<prev • 303 results • page 1 of 31 • next >
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Comment: C: Methylation-Gene expression correlation
... I am not familiar with this, but try to find a way to do binary logistic regression ...
written 7 weeks ago by nazaninhoseinkhan410
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Comment: C: Methylation-Gene expression correlation
... I used log transformed form of htseq-count data for gene expression and B values of methylation for corresponding genes for pearson correlation in R. Then I used <= - 0.5 for selecting significant negative correlations. When previously I had compared deregulated expressed genes and demethylated g ...
written 7 weeks ago by nazaninhoseinkhan410
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Comment: C: Methylation-Gene expression correlation
... Hi Kevin, I could solve the problem in R a few weeks ago, however I could find only one significant negative correlation! It is strange, isn't it? ...
written 7 weeks ago by nazaninhoseinkhan410
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Comment: C: visualizing mutational data using Maftools for reference genome hg19
... Hi, After running "`maf <- GDCquery_Maf("CESC", pipelines = "mutect") %>% read.maf"`, I get this : - ------------------------------------- o GDCquery: Searching in GDC database -------------------------------------- Genome of reference: hg38 ----------------------------- ...
written 7 weeks ago by nazaninhoseinkhan410
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visualizing mutational data using Maftools for reference genome hg19
... Dear all, I am trying to do somatic variation analysis using TCGABiolinks package in R 3.6. I want to use hg19 version of human genome. However I could not find any way to visualize the results using Maftools. It seems Maftools has only been designed for hg38. The following is the punch of codes ...
visualize maftools snv hg19 written 7 weeks ago by nazaninhoseinkhan410
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Methylation-Gene expression correlation
... Dear all, I am trying to perform methylation-gene expression correlation analysis in R. After removing probes not mapped to any gene symbol, around 300000 probes remained. Considering the large number of samples (280), the correlation analysis generates a huge adjacency matrix that it is impossi ...
dna methylation gene expression correlation written 10 weeks ago by nazaninhoseinkhan410 • updated 7 weeks ago by Kevin Blighe66k
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Comment: C: Negative gene expression values in "Illumina HumanHT-12 WG-DASL V4.0 R2 expressi
... Hey Kevin, Trying to get histogram from data after normalization I got this error: Error in hist.default(y, breaks = 50, col = "skyblue", xlim = c(-20, 20)) : 'x' must be numeric However, I integrated the normalized data with other data and introduced them in to SVA to remove batch effects. E ...
written 5 months ago by nazaninhoseinkhan410
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Comment: C: Negative gene expression values in "Illumina HumanHT-12 WG-DASL V4.0 R2 expressi
... Hey Kevin, This is the results of class(x) and str(x): > class(x) [1] "EListRaw" attr(,"package") [1] "limma" > str(x) Formal class 'EListRaw' [package "limma"] with 1 slot ..@ .Data:List of 5 .. ..$ : chr "illumina" .. ..$ :'data.frame': 40 obs. of ...
written 5 months ago by nazaninhoseinkhan410
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Comment: C: Negative gene expression values in "Illumina HumanHT-12 WG-DASL V4.0 R2 expressi
... Hey Kevin, I had replaced "data" with x through the code, because I did not understand what is the "data": idatfiles <- dir(pattern="idat") bgxfile <- dir(pattern="bgx") x <- read.idat(idatfiles, bgxfile) x$other$Detection <- detectionPValues(x) propexpr(x) y <- neqc(x) and I c ...
written 5 months ago by nazaninhoseinkhan410
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Comment: C: Negative gene expression values in "Illumina HumanHT-12 WG-DASL V4.0 R2 expressi
... No Kevin, I don't think so. This is the punch of codes I used: idatfiles <- dir(pattern="idat") bgxfile <- dir(pattern="bgx") x <- read.idat(idatfiles, bgxfile) x$other$Detection <- detectionPValues(x) propexpr(data) y <- neqc(data) ...
written 5 months ago by nazaninhoseinkhan410

Latest awards to nazaninhoseinkhan

Popular Question 3 months ago, created a question with more than 1,000 views. For how to perform cross platform gene expression analysis
Popular Question 3 months ago, created a question with more than 1,000 views. For corresponding gene names for probeIDs
Popular Question 3 months ago, created a question with more than 1,000 views. For WGCNA module membership cutoff
Popular Question 3 months ago, created a question with more than 1,000 views. For How to map probeIDs to x and y coordinates when no .clf file is available
Popular Question 3 months ago, created a question with more than 1,000 views. For installing ACGH analysis packages in R
Popular Question 3 months ago, created a question with more than 1,000 views. For co-expression between transcription factors and their targets
Popular Question 4 months ago, created a question with more than 1,000 views. For co-expression between transcription factors and their targets
Popular Question 4 months ago, created a question with more than 1,000 views. For co-expression between transcription factors and their targets
Popular Question 4 months ago, created a question with more than 1,000 views. For WGCNA module membership cutoff
Popular Question 5 months ago, created a question with more than 1,000 views. For co-expression between transcription factors and their targets
Popular Question 5 months ago, created a question with more than 1,000 views. For co-expression between transcription factors and their targets
Popular Question 5 months ago, created a question with more than 1,000 views. For WGCNA module membership cutoff
Popular Question 5 months ago, created a question with more than 1,000 views. For co-expression between transcription factors and their targets
Popular Question 6 months ago, created a question with more than 1,000 views. For co-expression between transcription factors and their targets
Popular Question 6 months ago, created a question with more than 1,000 views. For co-expression between transcription factors and their targets
Popular Question 8 months ago, created a question with more than 1,000 views. For WGCNA module membership cutoff
Popular Question 8 months ago, created a question with more than 1,000 views. For co-expression between transcription factors and their targets
Popular Question 8 months ago, created a question with more than 1,000 views. For co-expression between transcription factors and their targets
Popular Question 9 months ago, created a question with more than 1,000 views. For co-expression between transcription factors and their targets
Popular Question 10 months ago, created a question with more than 1,000 views. For Downloading data from TCGA
Popular Question 10 months ago, created a question with more than 1,000 views. For Downloading data from TCGA
Popular Question 11 months ago, created a question with more than 1,000 views. For Downloading data from TCGA
Popular Question 12 months ago, created a question with more than 1,000 views. For Downloading data from TCGA
Popular Question 12 months ago, created a question with more than 1,000 views. For Downloading data from TCGA
Popular Question 13 months ago, created a question with more than 1,000 views. For Downloading data from TCGA

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