User: chowdhury

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chowdhury0
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Posts by chowdhury

<prev • 6 results • page 1 of 1 • next >
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Comment: A: 50000 significant p values
... I have ADNI microarray dataset (https://ida.loni.usc.edu/pages/access/geneticData.jsp#207). The paper says it is normalized data. I have used R -limma package to do the expression analysis among healthy controls and patients. It has around 50000 probe set and sample size of 700 (equal amount of cont ...
written 11 months ago by chowdhury0
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50000 significant p values
... I have ADNI microarray dataset (https://ida.loni.usc.edu/pages/access/geneticData.jsp#207). The paper says it is normalized data. I have used R -limma package to do the expression analysis among healthy controls and patients. It has around 50000 probe set and sample size of 700 (equal amount of con ...
R microarray pvalue written 11 months ago by chowdhury0
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TCGA data and Sample size
... Hi, I am new to statistics and bioinformatics. I have a very basic question regarding sample size. If I'm using TCGA data, and I select 600 lung cancer samples for expression analysis and along with it I select 60 adjacent control data (paired data). Will I get an error in the result (false positiv ...
sample size tcga statistics written 14 months ago by chowdhury0 • updated 11 days ago by Kritika170
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Answer: A: Problem with Saminfo files
... Thank You for the reply. I have a question.I have fixed the sam parsing error. The size is around 55 gb for sam files and 6gb for sorted bam files.I have submitted sam to direct bam conversion as a job and in the error file, I am getting the following message: "SAM Tools version 0.1.18 loaded. **[sa ...
written 15 months ago by chowdhury0
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Problem with Saminfo files
... I have 2 questions. 1. I am working on RNA-seq data and using Hisat. I am submitting it as job. my script is `hisat2 -p 55 -x -q (to recognize fastq) -1 -2 -S /path/xyz.sam &> /path/xyz.sam.info` (I worked with the same command but never had problem) **I am getting sam files but my sam ...
rna-seq written 16 months ago by chowdhury0
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(Closed) box plot problem
... Hi,  I am trying to do a boxplot in R with normalized TCGA data. I am not getting the box diagram, instead I am getting a different image. Can anyone suggest where did I go wrong.The y axis range is 8-11. code: boxplot(x, las=2) Thanks R ...
R written 2.1 years ago by chowdhury0 • updated 2.1 years ago by Chris Miller19k

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