User: UserAnonyme

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Posts by UserAnonyme

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Comment: C: Difference between gene-level test and transcript-level test with RATs (Relative
... No it was just to see an example with a single gene, I have the scaled TPM for all of the genes ...
written 3 months ago by UserAnonyme0
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Comment: C: Difference between gene-level test and transcript-level test with RATs (Relative
... Ok, thank's ! :-) I compare my list od DEG and my list of DTU, and the overlap is small, so the exemple that I used ( obsx= c(100, 200, 300), obsy= c(5000, 200, 300) ) is maybe rare biologically speaking When I compare the results with rMATS the overlap with RATs is way better ( not surprising as ...
written 3 months ago by UserAnonyme0
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Comment: C: Difference between gene-level test and transcript-level test with RATs (Relative
... Thank's for this explanation, I see better ! I have a last question, for exemple in a gene-level test we have this abundances for the 3 transcripts between 2 conditions: g.test.2(obsx= c(100, 200, 300), obsy= c(5000, 200, 300)) The g.test.2 will be significative only because the first transcript ...
written 3 months ago by UserAnonyme0
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Comment: C: Difference between gene-level test and transcript-level test with RATs (Relative
... I have deleted the post on biostar ...
written 3 months ago by UserAnonyme0
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Difference between gene-level test and transcript-level test with RATs (Relative Abundance of Transcrits)
... Hi I'm trying to achieve a Differential Transcript Usage (DTU) analysis, in order to find genes that are differently alternatively spliced between my two conditions. The package RATs seems to allow this and I saw that two methods were used to find DTU genes: > At the gene level, RATs compares ...
rna-seq expression isoforms dtu rats written 3 months ago by UserAnonyme0 • updated 3 months ago by fruce_ki20
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Comment: C: Two factors design with DESEq2
... I had the interaction term on the design formula and so I have multiple set of genes: DEG for the effect of treatment in my WT DEG for the effect of treatment in my mutant DEG for diff between WT and mutant (no treatment) DEG for diff between WT and mutant (treatment) and finally: DEG for the diff ...
written 6 months ago by UserAnonyme0
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Two factors design with DESEq2
... Hi ! I have a RNAseq samples with this design: sample genotype traitement Col_1 wt normal Col_2 wt normal Col_3. wt normal ColHS_1 wt heat_shock ColHS_2, wt heat_shock ColHS_3 wt heat_shock hon4_1 hon4 normal hon4_2 hon4 normal hon4_3. h ...
deseq2 expression genes written 6 months ago by UserAnonyme0 • updated 6 months ago by Michael Love25k

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