User: Sakshi Gulati

gravatar for Sakshi Gulati
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6 years, 7 months ago
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6 years, 7 months ago
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s************@cancer.org.uk

Posts by Sakshi Gulati

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Comment: C: Is there any prejudice whether to use edgeR or DESeq for differential expression
... Hi Aaron, Yes, I had indeed rounded them up to avoid the non-integer issue as well. But, as the others pointed out, do you think it is an issue for me to use them in packages like edgeR or DESeq? Thanks Sakshi From: ajmackey@gmail.com [mailto:ajmackey@gmail.com] On Behalf Of Aaron Mackey Sent: 07 ...
written 6.6 years ago by Sakshi Gulati40
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Comment: C: Is there any prejudice whether to use edgeR or DESeq for differential expression
... Hi Mark, Thanks for answering. It makes more sense now. I have upper quartile normalised RSEM counts per gene. Is that ok as an input for edgeR and/or DESeq? Thanks Sakshi -----Original Message----- From: Mark Robinson [mailto:mark.robinson@imls.uzh.ch] Sent: 07 November 2012 13:18 To: Sakshi Gul ...
written 6.6 years ago by Sakshi Gulati40
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Is there any prejudice whether to use edgeR or DESeq for differential expression analysis for RNA Seq data
... Hi I am unsure as to if there is any particular condition that is the deciding factor between whether to use edgeR or DESeq packages for differential expression analysis for RNA Seq data. For example, does it depend upon how the counts were normalized? Thanks Sakshi Sakshi Gulati PhD Student Bio ...
edger deseq written 6.6 years ago by Sakshi Gulati40 • updated 6.6 years ago by Mark Robinson870
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DGEList and exactTest function in edgeR package
... Hi I am a novice for RNA Seq data analysis, and I am trying to compare groups which belong to more than 2 groups. I am unsure whether I have to specify this in 'DGEList' function or the 'exactTest' function, and how exactly to specify this? For example it may have 3 categories : Tumour_typeA, Norma ...
written 6.6 years ago by Sakshi Gulati40 • updated 6.6 years ago by Mark Robinson870

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