User: nazaninhoseinkhan

Reputation:
400
Status:
Trusted
Location:
Iran, Islamic Republic Of
Last seen:
2 weeks, 5 days ago
Joined:
6 years, 7 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 • 297 results • page 1 of 30 • next >
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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 6 weeks ago by nazaninhoseinkhan400
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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 6 weeks ago by nazaninhoseinkhan400
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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 6 weeks ago by nazaninhoseinkhan400
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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 6 weeks ago by nazaninhoseinkhan400
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Comment: C: Negative gene expression values in "Illumina HumanHT-12 WG-DASL V4.0 R2 expressi
... I normalized the data using limma and neqc() function in R 3.5.0 . Though the majority of values are 8.9. It is strange! ...
written 6 weeks ago by nazaninhoseinkhan400
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Comment: C: Negative gene expression values in "Illumina HumanHT-12 WG-DASL V4.0 R2 expressi
... So doing this will shift the distribution from normal (bell shape) and then t-test can not be applied? ...
written 6 weeks ago by nazaninhoseinkhan400
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Comment: C: Negative gene expression values in "Illumina HumanHT-12 WG-DASL V4.0 R2 expressi
... I need normalized expression values of this data set. Since several other data sets are present in my study, I need to remove batch effects from all using SVA package. I wanted to use limma package to analyze raw data, however bgx files was not available. This bgx file is required by read.idat() f ...
written 6 weeks ago by nazaninhoseinkhan400
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Comment: A: Negative gene expression values in "Illumina HumanHT-12 WG-DASL V4.0 R2 expressi
... Hi Kevin, Id:GSE93825 ...
written 6 weeks ago by nazaninhoseinkhan400
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Negative gene expression values in "Illumina HumanHT-12 WG-DASL V4.0 R2 expression beadchip"
... Dear all, I am trying to analyze an "Illumina HumanHT-12 WG-DASL V4.0 R2 expression" beadchip. However, when I open the non normalized data series, several negative values are present. Most of them are very large(for example, -20) Please guide me how should I deal with these negative values. I ...
negative expression values written 6 weeks ago by nazaninhoseinkhan400 • updated 6 weeks ago by Kevin Blighe61k
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Comment: C: several copy number alterations in the same position in an individual
... Hey Kevin, thanks for your comments ...
written 7 weeks ago by nazaninhoseinkhan400

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Popular Question 25 days ago, created a question with more than 1,000 views. For WGCNA module membership cutoff
Popular Question 25 days ago, created a question with more than 1,000 views. For co-expression between transcription factors and their targets
Popular Question 5 weeks ago, created a question with more than 1,000 views. For co-expression between transcription factors and their targets
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Popular Question 7 weeks ago, created a question with more than 1,000 views. For WGCNA module membership cutoff
Popular Question 8 weeks ago, created a question with more than 1,000 views. For co-expression between transcription factors and their targets
Popular Question 8 weeks ago, created a question with more than 1,000 views. For co-expression between transcription factors and their targets
Popular Question 9 weeks 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 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 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 Downloading data from TCGA
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Popular Question 9 months ago, created a question with more than 1,000 views. For Difficulty in getting GTF file from iGenomes
Popular Question 9 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 Difficulty in getting GTF file from iGenomes
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 co-expression between transcription factors and their targets
Popular Question 10 months ago, created a question with more than 1,000 views. For Difficulty in getting GTF file from iGenomes
Popular Question 10 months ago, created a question with more than 1,000 views. For Downloading data from TCGA

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