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Old 04-09-2014, 02:55 PM   #1
TheSeqGeek
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Default Normalized Values from DESeq2

This is the raw table example of my data but....

Gene Name Mutant Mutant Mutant WT WT WT
A 2343 2341 2842 1549 1303 1123

Can I get a table that has these normalized from DESeq2

Last edited by TheSeqGeek; 04-09-2014 at 09:22 PM.
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Old 04-09-2014, 05:09 PM   #2
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is this correct? or is this for the previous version of DESeq


normalizedCounts <- t( t(counts(dds)) / sizeFactors(dds) )

Last edited by TheSeqGeek; 04-09-2014 at 07:17 PM.
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Old 04-10-2014, 12:24 AM   #3
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Code:
counts(dds, normalized=T)
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Old 04-11-2014, 08:26 AM   #4
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Quote:
Originally Posted by dpryan View Post
Code:
counts(dds, normalized=T)
Thank you

Those two codes give the same results... Do you know why when I take the normalized to values and perform a log2fold change it is not the same as in DESeq2 log2foldchange


1.) take average of three replicates for mutant
2.) take average of three replicates for wt
3.) log2(mutatnt) - log2(wt)

This comes close to DESeq2 log2fold change but not quite the same...
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Old 04-11-2014, 08:46 AM   #5
dpryan
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It'll be a little off due to fold-change shrinkage (i.e., your calculated values should generally be larger).
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Old 04-11-2014, 11:09 AM   #6
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Quote:
Originally Posted by dpryan View Post
It'll be a little off due to fold-change shrinkage (i.e., your calculated values should generally be larger).
Indeed that is the case.

Thank you
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