User: Sandhya Pemmasani Kiran

Reputation:
40
Status:
New User
Location:
India
Last seen:
1 year ago
Joined:
6 years, 7 months ago
Email:
s********@ocimumbio.com

Posts by Sandhya Pemmasani Kiran

<prev • 6 results • page 1 of 1 • next >
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Comment: C: LIMMA on matched time series data
... Hi Aaron, Firstly, sorry for the mistake in design matrix. Here is the corrected one. FileName    Subject    Group    Time Ctrl_0h_Rep1    R1    Ctrl    0 Ctrl_0h_Rep2    R2    Ctrl    0 Ctrl_0h_Rep3    R3    Ctrl    0 T1_12h_Rep1    R1    T1    12 T1_12h_Rep2    R2    T1    12 T1_12h_Rep3    R3   ...
written 4.3 years ago by Sandhya Pemmasani Kiran40
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LIMMA on matched time series data
... Hi, I have timecourse microarray data generated from cell culture experiment. Three replicates were taken from the culture (three biological replicates - R1, R2 and R3), and, further on each replicate three treatments were given (T1, T2 and T3). For each treatment, cells were harvested at 12hrs, 24 ...
timecourse limma written 4.3 years ago by Sandhya Pemmasani Kiran40 • updated 4.3 years ago by Aaron Lun25k
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Comment: C: LIMMA on RT-PCR data
... Hi Gordon and Ryan, Thank you so much for all your help. Relieved after knowing that I can use limma on this gene set, because for microarray I used limma. This is validation experiment with RT PCR. So I wanted to maintain uniformity (if that makes sense) My experimental design is spread across 8 ...
written 6.0 years ago by Sandhya Pemmasani Kiran40
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LIMMA on RT-PCR data
... Dear list, I have RT-PCR data on 4 genes and 85 samples. Can I use 'limma' on this small set of genes? I want to use limma rather than usual paired t-test because I have missing values and I don't want to miss the information available on paired samples.. Please advise. Thanks, Sandhya ...
limma pcr written 6.0 years ago by Sandhya Pemmasani Kiran40 • updated 17 months ago by Gordon Smyth39k
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Identifying expression trends in RNA-seq experiment - through edgeR
... Hi all, We have data from RNA-seq experiment conducted on two siRNA knockdowns. Three conditions - Control, si1 and si2. Four doses - D0, D1, D2 and D3. There were no replicates. Total 12 samples. We are trying to use edgeR to identify differentially regulated genes. Since edgeR doesn't give p- ...
edger dose written 6.4 years ago by Sandhya Pemmasani Kiran40
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Question on unbalanced paired design
... Dear List: We are analyzing Agilent microarray data for a study where samples are related. After Quantile normalization on 'gProcessedSignal', averaging replicate spots and log transformation, we are trying to use LIMMA for differential expression analysis. Design is as follows- 4 Treatment group ...
microarray normalization go limma dose written 6.6 years ago by Sandhya Pemmasani Kiran40 • updated 6.6 years ago by Ryan C. Thompson7.4k

Latest awards to Sandhya Pemmasani Kiran

Popular Question 4.2 years ago, created a question with more than 1,000 views. For Question on unbalanced paired design
Popular Question 4.2 years ago, created a question with more than 1,000 views. For LIMMA on RT-PCR data
Popular Question 4.2 years ago, created a question with more than 1,000 views. For LIMMA on matched time series data

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