User: Konstantin Okonechnikov

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Posts by Konstantin Okonechnikov

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Comment: C: Issues with DEXSeq: rows did not converge in beta
... Hi Alejandro, number of NAs was 68028 (~11%) for p-value and 70609 (~12%) for log2fold_conditon  (total number of exons 588569). Indeed, I did not perform any initial  filtering like excluding not-expressed genes. Is there a suitable strategy for the filtering before analysis? ...
written 19 months ago by Konstantin Okonechnikov0
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Issues with DEXSeq: rows did not converge in beta
... HI!  I am using DEXSeq to compare exons within two conditions. The applied strategy was the same as in tutorial. However, after running testForDEU(...) function the following messages were reported: using supplied model matrix 5 rows did not converge in beta, labelled in mcols(object)$fullBetaCo ...
rnaseq dexseq written 19 months ago by Konstantin Okonechnikov0
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Comment: C: DESeq2: one condition vs multiple combined
... Thanks a lot for quick and detailed reply! ...
written 2.1 years ago by Konstantin Okonechnikov0
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DESeq2: one condition vs multiple combined
... I have multiple RNA-seq samples from 6 conditions and have to compare each condition against all the others: find genes dominant only in a specific group. I tried two approaches. First approach: separate all samples in 2 conditions: samples from one group vs samples from other groups, then repeat ...
rnaseq deseq2 written 2.1 years ago by Konstantin Okonechnikov0 • updated 6 months ago by rammohanshukla10

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Popular Question 18 months ago, created a question with more than 1,000 views. For DESeq2: one condition vs multiple combined

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