User: altintas.ali

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Posts by altintas.ali

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Comment: C: Is Limma's removeBatchEffect() and log2() commutative?
... Dear Gordon, By any chance, should `contr.sum` set to be `2` instead of `10` as it should be the `length` of batch `levels` according to the example given by Aaron? PS: I know this is an old post, but I hope you will see this. ...
written 5 months ago by altintas.ali0
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Comment: C: Re-numbering blocking IDs on paired samples with duplicateCorrelation or design
... Dear Aaron, Thank you very much for your detailed answers. Your solution for Question 1 (`~ 0 + Patient + Group`) is very neat. Just for me to understand it better: Let's assume that we have the same individuals sampled before and after they are sick (for some weird reason): ``` meta <- data.fr ...
written 5 months ago by altintas.ali0
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Re-numbering blocking IDs on paired samples with duplicateCorrelation or design covariate
... Hi all, I have a paired setup where there are healthy and sick individuals. They have received some treatment in a controlled fashion and I am interested in differential gene expression across treatment and disease groups. I was wondering whether I should use `edgeR` with blocking patient IDs in th ...
limma edger duplicatecorrelation batch effect written 5 months ago by altintas.ali0 • updated 5 months ago by Aaron Lun25k
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Comment: C: logCPM to CPM conversion after removeBatchEffect()
... Hi Aaron, I am grateful to you for your kind and detailed answers. Regarding to: **Question 1:** You are definitely right. When I was simulating the counts, I have also come across to negative un-logged CPMs when the `mu` and `size` parameters for `rnbinom` are low. ``` nsamples <- 12 ngenes ...
written 6 months ago by altintas.ali0
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Comment: C: logCPM to CPM conversion after removeBatchEffect()
... Hi Aaron, Thank you very much for your answers. If I may, I have some follow-up questions: **Question 1:** The solution 1 you have provided is a very elegant way of getting the pseudo-counts and I will be using that for CPM calculation if needed. Could you also help me to understand what I was mis ...
written 6 months ago by altintas.ali0
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Comment: C: logCPM to CPM conversion after removeBatchEffect()
... Hi Aaron, Sorry for not stating "why". Some downstream analysis tools like [DODR](https://cran.r-project.org/web/packages/DODR/index.html), [CIBERSORT](https://cibersort.stanford.edu/) etc. accept only non-logarithmic values. Knowing that there is a clear batch effect in my dataset, I didn't want t ...
written 6 months ago by altintas.ali0
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logCPM to CPM conversion after removeBatchEffect()
... Dear all, I was wondering if it is possible to convert logCPM values to CPM values after removing the batch effects using `removeBatchEffect` since it only returns logCPM values. # Problem As Aaron stated in [this post](https://support.bioconductor.org/p/107719/), it is not a good idea to convert ...
limma edger cpm removebatcheffect logcpm written 6 months ago by altintas.ali0

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