User: gtechbio

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Posts by gtechbio

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Comment: C: Allele-specific expression with different gene lenghts
... Hi Michael, Thanks for reply. Just to make sure I do everything in order: My `count_table` looks like SC1 SC2 SC3 SU1 SU2 SU3 YBR177C_Sbay_4.429 2711 3397 3765 1246 2156 3287 YIL140W_Sbay_9.48 178 111 204 109 271 250 Y ...
written 35 minutes ago by gtechbio0
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Allele-specific expression with different gene lenghts
... Hi, I want to use DESeq2 for assessing allele-specific expression. I will compare gene-level allelic counts of a yeast hybrid (basically comparing counts of orthologous genes of parentals of this hybrid). I'm aware of this tutorial http://rstudio-pubs-static.s3.amazonaws.com/275642_e9d578fe1f7a404aa ...
rnaseq deseq2 allele-specific-expression written 2 days ago by gtechbio0 • updated 1 day ago by Michael Love17k
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Comment: C: Time course DE analysis in DESeq2 with Wald test
... Thanks for your time Michael and sorry for coming back to you late. As far as I understand, with LRT the software will find a gene which became differentially expressed at any time point. In this case we assume, that if gene is changing its expression, this change is always towards one direction - ...
written 5 months ago by gtechbio0
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Comment: C: Time course DE analysis in DESeq2 with Wald test
... Hi Michael, thank you for your reply. Could you also please point out what is the conceptual difference between this approach and LRT-based time-course analysis, and whether any of those has advantages or disadvantages over another? And one more question regarding shrinkage (sorry if a silly one): ...
written 5 months ago by gtechbio0
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Time course DE analysis in DESeq2 with Wald test
... Hi All, This is to make sure I do a correct thing (which might be actually wrong). I have a time series experiment: 0 time point - yeast is growing alone (control), 3,12,24h time point - yeast is growing on human cells, and 24h (control) - yeast is growing alone. I need to do a time-series DE anal ...
deseq2 time-series written 5 months ago by gtechbio0 • updated 5 months ago by Michael Love17k
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Comment: C: DESeq2 for ASE
... Hi Michael, Thanks for reply! As far as I understand, in your example there are two conditions, while my case actually the are no conditions - I just need to compare ref and alt counts. So `condition` in my formula represents the alleles in fact. In this situation do you think the above analysis is ...
written 7 months ago by gtechbio0
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DESeq2 for ASE
... Dear all, My question was partially addressed in similar threads, but I'd like to raise the point one more time. I have read counts that come form RNAseq data, which was mapped to diploid genome of hybrid yeast (there are 3 biological replicates), thus I have counts for both parental homologs.    ...
deseq2 ase diploid-genome written 7 months ago by gtechbio0 • updated 7 months ago by Michael Love17k

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