User: sara.blocquiaux

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Posts by sara.blocquiaux

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Comment: C: SVA for repeated measures design
... I agree, that was what I was thinking at first. But subject.ID is not just a covariate, it is a random factor. So it is still not clear to me whether to include it in the null model or not. Not including it in the null model, makes it kind of a variable of interest itself. ...
written 6 weeks ago by sara.blocquiaux0
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Comment: C: SVA for repeated measures design
... Thanks James. Yes, I have repeated measures. Subject.ID is not my factor of interest, but of course I want to include it in the model. For one subject, I have two missing time points though. I do not want ComBat to correct for Subject.ID, but rather want SVAseq to find confounding factors (other ...
written 6 weeks ago by sara.blocquiaux0
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Comment: C: paired sample - SVA model matrix
... @flippy23 How did you finally designed the full and null model? Did you incorporate Study_ID in both the full and null model or only in the full model? mod = ~ Subject_ID + Treatment mod0 = ~ Subject_ID OR mod = ~ Subject_ID + Treatment mod0 = ~1 ...
written 6 weeks ago by sara.blocquiaux0
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Comment: C: surrogate variables from sva independent of model variables?
... I have the same problem. Did you manage to find an answer Esther? ...
written 6 weeks ago by sara.blocquiaux0
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Answer: A: DESeq2: Internal reference and multiple comparisons
... Could you treat the control 'genes' as non-differentially expressed genes over time and conditions and normalize the rest of the data with these control genes? This method is called normalization with housekeeping genes. *"Housekeeping genes (HG) are genes that play a role in the basic functions o ...
written 7 weeks ago by sara.blocquiaux0
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SVA for repeated measures design
... Hi all, I have RNA-seq data (5 subjects are measured on 4 time points) and would like to do a SVA first to be able to include potential confounders into the statistical model (Deseq2 pipeline). I am having troubles how to define my null and full model in the SVA: Full model ~ TIME + SUBJECT.ID ...
sva deseq2 repeated measures written 7 weeks ago by sara.blocquiaux0 • updated 6 weeks ago by Robert Castelo2.3k
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Bioconductor SVA: two variables of interest
... Dear Bioconductor list & Jeff Leek, I am using the sva function in the SVA package to estimate surrogate variables in my methylation data (EPIC beadchip, Illumina). The main goal is to define the effect of time & group (and their interaction) on methylation. I was wondering how to incorpora ...
sva written 10 weeks ago by sara.blocquiaux0 • updated 10 weeks ago by James W. MacDonald51k
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Combining pfilter (wateRmelon) and preprocessNoob (minfi)
... Dear all, I want to combine the packages minfi and wateRmelon to analyse my EPIC methylation data. I loaded my data as an RGChannelSetExtended into R with Minfi. Next I wanted to filter out low quality samples and probes with the pfilter function of wateRmelon. Downside: the function returns a Met ...
minfi watermelon methylation pfilter preprocessnoob written 11 weeks ago by sara.blocquiaux0 • updated 11 weeks ago by tgorri10

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