User: udp3f

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udp3f0
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Posts by udp3f

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Comment: C: DEseq2 - design help
... Well, I have no results at all for (with a Padj<0.05) ``` results(dds, name="drugpro.treatmentS") results(dds, name="drugiso.treatmentS") results(dds, contrast=list("drugiso.treatmentS", "drugpro.treatmentS")) ``` but, have results for (I am interested to know what question this output answers? ...
written 9 weeks ago by udp3f0
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Comment: C: DEseq2 - design help
... Ok thanks! Can you please answer how the below results for the design you suggested are different ``` names= "drug_pro_vs_iso" & contrast=list("drugpro.treatmentS","drugiso.treatmentS") ``` I see that I did not get any differentially expressed genes for any of these below ``` results(dds, name= ...
written 9 weeks ago by udp3f0
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Comment: C: DEseq2 - design help
... Hi Michael, Thank you for your reply. That was extremely helpful. I seemed to have overlooked the example which was for a paired design. One other question is, is there no need to account for the sample specific effects? Also, with what you suggested resultsNames(dds) gives ``` resultsNames(dds) ...
written 9 weeks ago by udp3f0
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Comment: C: DEseq2 - design help
... Hi Michael, Sorry if that was confusing. Considering the first 2 rows, the 2 samples do not have anything in common. For the metadata, I paired the control and test groups randomly to add an extra column "sample.nested" and later accounted for them, following a post as in https://support.bioconduc ...
written 9 weeks ago by udp3f0
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DEseq2 - design help
... Hi, I have the following design where each sample is pooled from many samples and the control and treated(S) samples are not paired. I want genes that are differentially expressed under the effect of the 2 drugs for treatment S. I created 'sample.nested' to account for the pairing of control and tr ...
deseq2 written 9 weeks ago by udp3f0 • updated 9 weeks ago by Michael Love23k
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Differential expression across time points
... Hi, I have a study design with 2 biological replicates where I want to know the differentially expressed genes in each of these across different time points.  sample state Days A DIAGNOSIS 0 A RELAPSE1 100 A RELPASE2 300 B DIA ...
deseq2 written 10 months ago by udp3f0 • updated 10 months ago by Michael Love23k

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