User: naets_matthias

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Posts by naets_matthias

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Comment: C: DESeq2 count normalization
... Michael, thank you for all the effort you put in. Your suggestions have been very valuable. ...
written 17 months ago by naets_matthias0
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Comment: C: DESeq2 count normalization
... I don't think this looks good... You even get the same image when you would plot the 3rd mock of 28 hrs against another mock of 28 hrs... ...
written 18 months ago by naets_matthias0
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Comment: C: DESeq2 count normalization
... Yes, I can see how that's confusing. Here is the plot with aggressive filtering and down sampling combined. Since it has hardly changed, I just showed the plot above. I use the rlog transformation and not the VST. ...
written 18 months ago by naets_matthias0
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Comment: C: DESeq2 count normalization
... Dear Michael, thank you for your many suggestions already. I tried down sampling using the thinCounts function from edgeR. This still didn't change much in the PCA plot. I've attached the plot (without down sampling) to show that those 4 samples show weird behavior. Having tried all this, I would st ...
written 18 months ago by naets_matthias0
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Comment: C: DESeq2 count normalization
... Increasing the filtering unfortunately didn't solve the problem... The medians of the log2(normalized counts) do align now, but the PCA remains the same. When analyzing the data I really have the feeling these samples often show high expression values when they shouldn't (and not just for genes expr ...
written 18 months ago by naets_matthias0
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Answer: A: masigpro Error in terms.formula(formula, data = data) : '.' in formula and no
... I also got the same error a few times, but never really figured out what caused it. Changing the step.method option from "backward" to "forward" did seem to solve the issue in one case. ...
written 18 months ago by naets_matthias0
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Comment: C: DESeq2 count normalization
... Hi Michael, Thank you for your quick reply. Indeed, these samples had a higher total read count. Especially the mock inoculated sample of 28 hrs, which had 7 times the value of most samples with around 70 million reads. The controls of 28 hrs had around 20 million reads, whereas most samples had ab ...
written 18 months ago by naets_matthias0
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DESeq2 count normalization
... Hi everyone, I am using DESeq2 to analyze my RNAseq data and really like the package. There is lots of information available, a very helping community, and the code is quite easy. However, I do seem to have one problem when it comes to my normalized read counts. It seems that four of my samples are ...
normalization deseq2 normalized counts written 18 months ago by naets_matthias0 • updated 18 months ago by Michael Love25k
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Comment: C: masigpro Error in terms.formula(formula, data = data) : '.' in formula and no
... Hi John, I am wondering whether you found a solution to your problem in the end? I recently also started using maSigPro and have encountered the exact same problem. After a lot of trying and looking around I still haven't managed to fix it... Kind regards, Matthias ...
written 22 months ago by naets_matthias0

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