User: heikki.sarin

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Posts by heikki.sarin

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Comment: C: RNA-seq: Time-course data normalisation with TPM
... Is there a way to implement this on a data frame with raw read counts (e.g. similar needed to DESeq2)? Or is it mandatory to go back on the original files? Not really that familiar with Salmon and how to use it (do you know there's a vignette manual but it's always a time consuming path to learn ne ...
written 4 months ago by heikki.sarin0
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RNA-seq: Time-course data normalisation with TPM
... I have RNA-seq time-course data (3 TP) with control/case design I'd like to do TPM normalization for the dataset but not quite sure what's the best way to apply it. Would it be most wise to 1) TPM normalize each time point individually and after that 2) normalize the whole dataset in one step? If so ...
normalization deseq2 rna-seq tpm written 4 months ago by heikki.sarin0 • updated 4 months ago by Michael Love18k
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Comment: C: DESeq2 model - How to test case/control time course model when taking account wi
... Can you explain why is that compared to the model where condition is also included? Why there isn't need for replicates per sample in that model? ~condition + time + condition:subject.nested + condition:time   ...
written 11 months ago by heikki.sarin0
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Comment: C: DESeq2: How to manually perform filtering and outlier detection?
... Yeah the former is my focus here. 1) I think one of the problems is that I used LRT-test. Do understand correctly that with LRT the "cooks distance" is not applied in the analysis? I have studied the "Cooks distance"-values but I'm not quite sure what threshold to use with manual filtering - they r ...
written 11 months ago by heikki.sarin0
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Comment: C: DESeq2 model - How to test case/control time course model when taking account wi
... Actually I have three timepoints for every subject and almost twenty biological replicates. Shouldn't it work? ...
written 11 months ago by heikki.sarin0
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Comment: C: DESeq2 model - How to test case/control time course model when taking account wi
... That's exactly what I was looking for. However, DESeq2 produces the following error : Warning message: In checkForExperimentalReplicates(object, modelMatrix) :   same number of samples and coefficients to fit,   estimating dispersion by treating samples as replicates.   read the ?DESeq section on ' ...
written 11 months ago by heikki.sarin0
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Comment: C: DESeq2 model - How to test case/control time course model when taking account wi
... Follow-up on this post. If I'd like to perform just case-only analysis with LRT between time-points would the correct models be: ~ subject.nested + time:subject.nested ~ subject.nested So that the between subject variability is taken into account. ...
written 11 months ago by heikki.sarin0
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DESeq2: How to manually perform filtering and outlier detection?
... Hi, I'm quite sure I have a problem with the DESeq2 independent filtering. DESeq2 doesn't flag any outliers when performing the DE analysis. We have little concern about blood being in the samples as the raw counts vary from hundreds to tens of thousands in some HB related genes. For some reason DE ...
deseq2 outliers filtering count outliers written 11 months ago by heikki.sarin0 • updated 11 months ago by Wolfgang Huber13k
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RUVseq: How to implement to more complex time-course model?
... We have quite complex model in the analysis and was wondering about the RUVseq argument "k". Should it be set to 1 or how many in this case below (the vignette isn't really helpful in modifying the example code) ? And is the below right way to implement the W_1 in the model of differential expressio ...
deseq2 ruvseq model.matrix confounders written 11 months ago by heikki.sarin0 • updated 11 months ago by davide risso740
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Comment: C: Dealing with (blood) contamination in RNA-seq data
...     Thank you very much for the help. Going to examine both approaches and see if the results make sense. We have quite complex model in the analysis and was wondering about the RUVseq argument "k". Should it be set to 1 or how many in this case below (the vignette isn't really helpful in modifyi ...
written 11 months ago by heikki.sarin0

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