User: loliveira

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loliveira0
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Posts by loliveira

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Comment: C: Large fold changes after deseq2 when one condition has two zeros and small numbe
... Hi Mike,  Thanks for lingering on,  I updated my DESeq2 to the latest version, and did exactly the same run as before, (as below) The first difference I noted was that now I see the citation to the manuscript (Nice paper!), the second is that the results for the lfcShrink changed dramatically. Now ...
written 6 months ago by loliveira0
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Comment: C: Large fold changes after deseq2 when one condition has two zeros and small numbe
... Thanks again for the support, I did add the lfcShrink to my datasets and relevel for each combination of variables. The results made much more sense now(Thank you). However, I still have several genes where  (ex. below from-Ctrl vs Infected 1wk) several genes are zeros on the CTRL and I have only on ...
written 6 months ago by loliveira0 • updated 6 months ago by Michael Love23k
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Comment: A: Large fold changes after deseq2 when one condition has two zeros and small numbe
...   Dear Michael,  Thanks for your reply, I need to do multiple comparing the  conditions, but when I try the coef= on the lfcShrink it restrict me to the resultsNames(dds) as below, Since I need more iterations I am considering going for the betaPrior=TRUE. What would you indicate in this case? Ho ...
written 6 months ago by loliveira0
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Large fold changes after deseq2 when one condition has two zeros and small number the other condition has two zeros and a large number
... I am working with 18 RNAseq datasets of 6 conditions in triplicates. I am importing the data from RSEM using TXimport and proceeding with  deseq2 - My question is that looking at the results for a preliminary comparison I see that I have high Log2fc (~20) and significant Padjust, however when I go t ...
rnaseq deseq2 rsem written 7 months ago by loliveira0

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