User: immunogirl2

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immunogirl220
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Posts by immunogirl2

<prev • 10 results • page 1 of 1 • next >
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Comment: C: Differential expression analysis error - TCGAbiolinks
... No, I did not try, yet. But, I'll try to give it a go. I was working on manually curated datasets (patient IDs divided based on clinical features). I tried codes on several different sets, sometime it works, sometimes it doesn't. ...
written 7 weeks ago by immunogirl220
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Comment: C: Differential expression analysis error - TCGAbiolinks
... Hi Kevin, is there any update on this issue? i am also facing the same issue [Error in dataFilt[, samples] : subscript out of bounds)]. Thanks in advance. ...
written 7 weeks ago by immunogirl220
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DESeq2 of log2(count+1) transformed TCGA htseq counts from Xenabrowser
... Hi, Can I use log2(count+1) transformed TCGA htseq counts from Xenabrowser directly for DESeq2 analysis? Or, do i need to reverse transform the data? Please point me out any R script to reverse transform the file. Thanks in advance. ...
R rna-seq written 9 weeks ago by immunogirl220 • updated 9 weeks ago by antonioggsousa1.4k
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Comment: C: FireBrowse TCGA data files
... Thank you. One additional Q, do i need to use Tximport with that file or can use this file directly in DESeqdatasetfrommatrix? ...
written 9 weeks ago by immunogirl220
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FireBrowse TCGA data files
... Which FireBrowse file type (TCGA RNAseq data) is suitable to be used with DESeq2. When I use 'RSEM_genes' (unnormalized) file I get 'not all values integer' msg.![please see the image][1] [1]: http://zyxue.github.io/assets/KICH-FireBrowse-mRNA-analysis-results-files.png ...
R rna-seq written 9 weeks ago by immunogirl220 • updated 9 weeks ago by Shalu Jhanwar470
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Comment: C: Very high FPKM values (snoRNA) in RNAseq data
... Thanks a lot. I'll make sure if QC and analysis is correct. ...
written 6 months ago by immunogirl220
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Very high FPKM values (snoRNA) in RNAseq data
... Recently I got RNA-seq data and found following kind of FPKM values in several samples for a "Small Nucleolar RNA" gene: FPKM value : 1.84E+08, 7.56E+07............ I think something went wrong (the library preparation, sequencing, and data analysis was performed by a commercial company). The exper ...
rna-seq written 6 months ago by immunogirl220
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Comment: C: TCGA data from Xena browser and Broad (GDAC Firehose)
... It worked fine. Thanks again. ...
written 8 months ago by immunogirl220
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Comment: C: TCGA data from Xena browser and Broad (GDAC Firehose)
... Thank a lot. I'll try as you suggested. ...
written 8 months ago by immunogirl220
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TCGA data from Xena browser and Broad (GDAC Firehose)
... I am an immunologist with very little background in bioinformatics; I can use basic functions in R. So, please bear with me. 1. I have classified TCGA breast cancer patient IDs based on their immune profiles into two groups. 2. I have downloaded TCGA breast cancer RNA-seq data from Xena and Firehose ...
R tcga rna-seq written 8 months ago by immunogirl220 • updated 8 months ago by Kevin Blighe65k

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