User: Nitesh Kumar Singh

Reputation:
30
Status:
New User
Location:
CCMB, Hyderabad, India
Last seen:
4 months, 2 weeks ago
Joined:
3 years, 7 months ago
Email:
n***********@yahoo.com

Posts by Nitesh Kumar Singh

<prev • 6 results • page 1 of 1 • next >
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Integer overflow issue with ChIPQC
... Hi, I have recently started working on ChIP-seq data. So after mapping using Bowtie and calling peak caller using MACS2, I wanted to do check the quality of peaks. For this, I used ChIPQC but I was getting error with ChIPQCreport. On checking I realized that ChipQCsample was returning nothing for "F ...
chipqc rstudio written 5 months ago by Nitesh Kumar Singh30 • updated 5 months ago by Martin Morgan ♦♦ 24k
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Comment: C: Understanding the design matrix
... Thanks Michael. I will follow your suggestion. ...
written 3.6 years ago by Nitesh Kumar Singh30
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Comment: C: Understanding the design matrix
... Hi, I am interested in the first one, DE at both time points. But can you explain how i can obtain DE for both the above cases, for learning purpose. Also, is there any link which will help me understand what i want to do? ...
written 3.6 years ago by Nitesh Kumar Singh30
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Comment: C: Understanding the design matrix
... Change in both should count. Is it same if I take union of DEGs between knockout and wild at 2hr and 4hr? I thought doing it at same time will have more statistical power. ...
written 3.6 years ago by Nitesh Kumar Singh30
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Comment: C: Understanding the design matrix
... Hi Michael, For knockout vs wild (both 2hr and 4hr), I meant that testing DEG between knockout and wild considering both time points (2hr and 4hr). So its overall change in expression pattern between experiments. Null hypothesis would be that there is no significant diff in expression pattern of ge ...
written 3.6 years ago by Nitesh Kumar Singh30
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Understanding the design matrix
... Hi, I always gets confused with the design matrix and even though I figure out the solution I am not very confident. So I though of asking for help.  I have 3 experiments: Control, wild and knockout. 2 time points: 2 and 4 hr. and 3 replicate for each. I am not sure which of the following design ...
deseq2 design and contrast matrix written 3.6 years ago by Nitesh Kumar Singh30 • updated 3.6 years ago by Michael Love26k

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