User: Shobana Sekar

gravatar for Shobana Sekar
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20
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New User
Location:
Phoenix, AZ
Last seen:
3 years, 3 months ago
Joined:
5 years, 7 months ago
Email:
s*****@tgen.org

Posts by Shobana Sekar

<prev • 4 results • page 1 of 1 • next >
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Answer: A: DESeq2 transformation to use for PCA plot
... Okay, thanks! I'll use the vst then for my PCA plots.  Thank you! ...
written 3.4 years ago by Shobana Sekar20
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DESeq2 transformation to use for PCA plot
... Hi, I created a PCA plot for our RNAseq count dataset following the instructions in the vignette, using r log transformation. Though my plot got generated, I got this warning message when I called the rlog function: Warning message: In sparseTest(counts(object, normalized = TRUE), 0.9, 100, 0.1) : ...
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Comment: C: DESeq2
... Thank you so much for the detailed answer! -Shobana From: Michael Love > Date: Tuesday, February 25, 2014 5:01 PM To: Shobana Sekar > Cc: "guest@bioconductor.org" >, "bioconductor@r-project.org" > Subject: Re: DESeq2 hi Shobana, I'm continuing our discussion where we left off on the ...
written 5.6 years ago by Shobana Sekar20
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Comment: C: DESeq2
... Hi Mike, Thank you for the quick reply. So when I filtered using the padj < 0.1 criterion, DESeq did not give me any results but DESeq2 showed 53 genes. But when I used the pval < 0.05 criterion and filtered, I got 1008 genes in DESeq2 and 222 genes in DESeq, with no overlap between the 2 lis ...
written 5.6 years ago by Shobana Sekar20

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