User: sasha

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sasha0
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Posts by sasha

<prev • 10 results • page 1 of 1 • next >
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Answer: A: Time points and donors - errors with contrasts
... Hi Michael, I realised just recently that the problem is related to the "SAN controllers" from the unix system (where I use R studio from) in my institute. They are actually having big problems at the moment. When I repeated everything in my R studio (in my personal computer) everything worked perf ...
written 2.2 years ago by sasha0
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Comment: A: Time points and donors - errors with contrasts
... Dear Michael, Thank you for your reply. I checked the character string as you suggested: > levels(DDS$TimePoint) [1] "T2" "T1" "T3" > resultsNames(DDS) [1] "Intercept" "Mother_Child1" "Mother_Child2" "Mother_Child3" "TimePoint1" "TimePoint2" Just to let you know, Mother_Child = D ...
written 2.2 years ago by sasha0 • updated 2.2 years ago by Michael Love25k
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Time points and donors - errors with contrasts
... Dear community, I've been trying to test if there are differentially expressed genes between different time-points of samples taken from the same donors. Experiment: SampleID      Donor     TimePoint A1                   1            T1 A2                   1            T2 A3                   ...
deseq2 contrast written 2.2 years ago by sasha0 • updated 22 months ago by Michael Love25k
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Answer: A: Difference between fitFeatureModel and fitZIG in metagenomeSeq
... Thanks to both handibles and Joseph ...
written 2.5 years ago by sasha0
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Difference between fitFeatureModel and fitZIG in metagenomeSeq
... Hi, I would like to know the differences between using fitFeatureModel and fitZIG when testing for DA using metagenomeSeq. I don't seem to find a good explanation of what fitFeatureModel does in detail and what are the differences with fitZIG, however, given that the authors (and others in the lite ...
metagenomeseq written 2.5 years ago by sasha0
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Has anyone used the RUV package for Microbiome data?
... Hi, I was wondering, has anyone used the RUV package for removing unwanted variation in microbiome data? I would be really interested in knowing about your experience doing it. Thanks in advance and cheers, Alexandra ...
ruv written 2.6 years ago by sasha0
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Comment: C: Design: DESeq2 and continuous variables
... Hi Simon, Thanks a lot for your answer, it helped me to understand things a lot better. Sasha ...
written 2.8 years ago by sasha0
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Comment: C: Design: DESeq2 and continuous variables
... Hi Simon, Sorry about that :( X is BMI (or Body mass index). This is a pregnancy study. We want to answer two things. a. Does the BMI at the beginning of the pregnancy has an influence in the expression of any gene? b.  Do different "weight gain levels" (i.e. kilograms gained) during pregnancy has ...
written 2.8 years ago by sasha0
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Answer: A: Design: DESeq2 and continuous variables
... Hi Simon, Sorry about that :( X is BMI (or Body mass index). This is a pregnancy study. We want to answer two things. a. Does the BMI at the beginning of the pregnancy has an influence in the expression of any gene? b.  Do different "weight gain levels" (i.e. kilograms gained) during pregnancy has ...
written 2.8 years ago by sasha0
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Design: DESeq2 and continuous variables
... Dear community, I'm trying to use DESeq2 to test if there is a relation between the expression of any genes and X (a continuous variable). For my design I have 5 persons and samples where taken from those at 3 different times. I think the design would be: ~ Persons + time + X Is this correct? Th ...
deseq2 written 2.8 years ago by sasha0 • updated 2.8 years ago by Simon Anders3.6k

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Popular Question 2.2 years ago, created a question with more than 1,000 views. For Design: DESeq2 and continuous variables
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Difference between fitFeatureModel and fitZIG in metagenomeSeq

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