User: anand m t

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anand m t40
Reputation:
40
Status:
New User
Location:
Singapore
Last seen:
2 years, 4 months ago
Joined:
7 years, 7 months ago
Email:
a*********@gmail.com

Posts by anand m t

<prev • 6 results • page 1 of 1 • next >
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DESeq2 - design for TCGA level 3 data
... Hi all, I am using TCGA level 3 data (rsem raw counts) for samples with matched normal to analyse differential expression using DESeq2. I was wondering the design I am using is correct. coldata looks like this.   DataFrame with 118 rows and 2 columns condition ...
deseq2 tcga multiple factor design experimental design written 3.9 years ago by anand m t40 • updated 3.9 years ago by Michael Love23k
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Comment: C: DESeq2 time series: error while measuring gene dispersion.
... Hi Mike, Thank you for a detailed description. I have updated my R and bioc. As you mentioned newer version (1.6.3) does give detailed error desciption. However I have some question. Since we don not have biological replicates (blame expensive technology!) first option is not possible. When you say ...
written 4.2 years ago by anand m t40
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DESeq2 time series: error while measuring gene dispersion.
... Hi all, I have been trying DESeq2 to analyse my RNAseq data. Data is from sequencing a cell line treated with a drug at different time point intervals. My sampleTable looks like this: DataFrame with 5 rows and 2 columns treatment time <factor> <factor> cl_0h untr ...
timecourse deseq2 written 4.2 years ago by anand m t40 • updated 4.2 years ago by Michael Love23k
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some basic questions
... Dear Dr. Friedman, Thank you for the notes again. It was really helpful and my many questions got cleared after going through it. But what my adviser asking me to do is, i've normalized data (54 k probes), he's asking me to functionally group them all. After that, he wants me to perform significanc ...
microarray annotation normalization cdf probe cycle written 7.4 years ago by anand m t40 • updated 7.4 years ago by Richard Friedman2.0k
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Comment: C: which statistical test to perform?
... Dear Sir, Thank you for your valuable suggestion. Will definitely look into it. I've one more question though. Sir, if we have only two datasets (say lung and liver), we can calculate log ratio (lung/liver) and finally fold change (2^log_ratio , considering log2 ratio). But in this case, if i want ...
written 7.4 years ago by anand m t40
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how to get probe ids??
... Hi all.. I'm very new to microarray analysis. i've been given two datasets for analysis. (experimental and control with 3 replicates each) I've encountered following errors/problems.. 1.whenever i tried to run mas5calls, it throws an error saying the presence of NA/Inf/NAN's in the data. > aff ...
microarray probe affy written 7.6 years ago by anand m t40 • updated 7.6 years ago by James W. MacDonald49k

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Popular Question 2.4 years ago, created a question with more than 1,000 views. For DESeq2 - design for TCGA level 3 data

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