User: wlorenz

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wlorenz0
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Posts by wlorenz

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Comment: C: DESeq2- Another Multi-factor Question
... Thanks, Michael.  One more question.  In the final dds1 object I created for the 2nd factor analyses above there is a result called Secondary_M_vs_F.  Can you describe exactly what this represents?  For example, if I output it as follows: res3 <- results(dds1, contrast=c("Secondary","M", "F")) a ...
written 4 weeks ago by wlorenz0
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DESeq2- Another Multi-factor Question
... I have a data set that I discovered had a secondary component (sex of the individuals) after I had already processed it without that factor. I went back and reran the analysis including the second factor (see META file below); however, the results are a bit perplexing and I'm trying to figure out i ...
deseq2 written 5 weeks ago by wlorenz0 • updated 4 weeks ago by Michael Love17k
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Comment: C: DESeq2: Extremely large log2 expression values with little or no read evidence
... Thank you for the code, I'll try it.  So, if I understand what you're saying (maybe not), the first gene in my example has other matrix groups (not being compared) with norm count values of 0 1 300, 0 57 0 and 0 133 1 and it is these groups and their lack of sufficient replication (is this impactin ...
written 4 months ago by wlorenz0
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Comment: C: DESeq2: Extremely large log2 expression values with little or no read evidence
... Thanks, Michael.  Just sent you an e-mail with DropBox link to data. ...
written 4 months ago by wlorenz0
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DESeq2: Extremely large log2 expression values with little or no read evidence
... I've tried to find if anyone else has seen this, but none describe what I'm seeing.  I have a pretty simple/small data set: 6 groups, 3 reps/group (2 ctrl and 4 exptl).  Read data were mapped to a Trinity assembly w/bt2 and the expected counts generated with RSEM (gene_results) were used to generate ...
deseq2 written 4 months ago by wlorenz0 • updated 4 months ago by Michael Love17k

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