User: arpit.singh1203

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Posts by arpit.singh1203

<prev • 16 results • page 1 of 2 • next >
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Comment: C: Human 450K array data and rnaseqv2 data
... I ran DESeq2 on my data and got zero DE genes. I think the following reasons could cause this: Data is taken from TCGA and only 3 samples are "Normal" while 65 are "Tumor". Not having replicates for the data. Do you think these could be the reasons? And is that why you suggested me to "compute ...
written 3.1 years ago by arpit.singh120360
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Comment: C: Human 450K array data and rnaseqv2 data
... Yes the 65 samples (Tumor) are matched with unique tcga ID. I am afraid I don't understand what you mean by co-relating rather than comparing. Could you please discuss a little more on that? ...
written 3.1 years ago by arpit.singh120360
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Human 450K array data and rnaseqv2 data
... Hello All "I had planned to carry out 450K human methylation data analysis and gene expression analysis to corelate differentially expressed genes to differentially methylated regions for publicly available cancer data from TCGA." I had used COHCAP to find DMRs in 75 samples (65 T + 10 N).[450 K h ...
rnaseq epigenetics cohcap edger written 3.1 years ago by arpit.singh120360
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Comment: C: Require review/comments/suggestions on 450k analysis college project
... Thanks a lot for the quick reply. ...
written 3.2 years ago by arpit.singh120360
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Comment: C: Require review/comments/suggestions on 450k analysis college project
... Thank you very much for the comments and suggestions. ...
written 3.2 years ago by arpit.singh120360
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Require review/comments/suggestions on 450k analysis college project
... Hello everyone I am a beginner level bioinformatician planning to work on "Analysing and interpreting the 450k methylation data for 70 odd samples from TCGA for a particular cancer". I intend to find DMRs when comparing tumor samples and normal samples. Later on I would like to co-relate the gene e ...
450k methylation minfi cohcap champ written 3.2 years ago by arpit.singh120360 • updated 12 months ago by allayza_cute0
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Comment: C: Memory allocation problems in 450k analysis
... Oh all right! I just thought maybe I could make-do by tweaking the code a little bit, which might increase the computational time. Is it possible? Could I break the process into smaller parts and solve this issue? ...
written 3.2 years ago by arpit.singh120360
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Memory allocation problems in 450k analysis
... I have 75 samples' data downloaded from TCGA. While running some of the steps in the pipelines like ChAMP, Minfi, etc., I get maximum memory allocation reached error. I have 4 GB RAM and i3 processor. Please suggest me possible alternatives or workarounds? Thanks much. ...
R minfi methylation champ written 3.2 years ago by arpit.singh120360 • updated 2.8 years ago by Shicheng Guo4.9k
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Infinium/Illumina 450K methylation array data analysis: How to compare the various packages/pipelines?
... Hello I am planning to work on 450K methylation array data. There are various pipelines/packages for data analysis. I don't need to know the best or the standard pipeline for the analysis. However I would appreciate ideas on how to compare various pipelines? For a sample data I can use minfi, ChAM ...
methylation minfi cohcap rnbeads champ written 3.4 years ago by arpit.singh120360 • updated 3.4 years ago by Charles Warden5.0k
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Comment: C: Human 450K methylation data: Tumor vs Normal vs Control
... I get your point. Thank you. ...
written 3.4 years ago by arpit.singh120360

Latest awards to arpit.singh1203

Popular Question 5 weeks ago, created a question with more than 1,000 views. For Human 450K methylation data: Tumor vs Normal vs Control
Popular Question 15 months ago, created a question with more than 1,000 views. For Human 450K methylation data: Tumor vs Normal vs Control
Supporter 3.1 years ago, voted at least 25 times.

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