User: SamGG

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SamGG • 180
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France
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Posts by SamGG

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Comment: C: Help with Limma F.p.value from eBayes
... Thanks for your reply and pointing the interesting post you wrote more than ten years ago (you are a library definitively). As answered also to Aaron, could you point me any **peer reviewed article** that discuss the benefits of carrying out t tests directly over the F-then-t strategy in the contex ...
written 8 days ago by SamGG • 180
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Comment: C: Help with Limma F.p.value from eBayes
... Thanks for your reply. In my case, the "F-test before t-test" strategy comes from the ANOVA. Could you point me any **peer reviewed article** that discuss the benefits of carrying out t tests directly over the F-then-t strategy in the context of high-dimensional data? Or is it a property of the lin ...
written 8 days ago by SamGG • 180
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Comment: C: Help with Limma F.p.value from eBayes
... Dear Aaron, May I ask you to comment the two following simulations based on your simulation concerning F vs t test. Here I increased the number of replicates from 2 to 4 and set the number of DE genes to 300. I don't feel any interest in estimating an effect with two samples. In that case, F is fin ...
written 9 days ago by SamGG • 180
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Comment: C: Flow cytometry optimization of transformation parameters
... Thanks for your reply. Let us know about your feedback and if you could publish your code, it could be helpful for the community. Best. ...
written 5 weeks ago by SamGG • 180
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Comment: C: Flow cytometry optimization of transformation parameters
... I agree totally. The parameters of the transformation should be the same for all the samples aka FCS. So pooling all FCS before estimating logicle is definitively what should be done within a batch, unless you have good reasons to do an estimation file by file. IIRC there is an alternative way to co ...
written 5 weeks ago by SamGG • 180
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Comment: C: Flow cytometry optimization of transformation parameters
... Hi Carlos, I think there are two points in your question. a) estimating the best set of parameters for a asinh transform: I don't know how to achieve this. Probably Mike and Greg do. b) looping across the channels: you could find the code of the estimateLogicle function at https://github.com/RGLa ...
written 5 weeks ago by SamGG • 180
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Comment: C: Dealing with NA values from mass spec data using Limma, NA values.
... Thanks a lot for making your answer even clearer. Some more questions arise. What is the floor intensity level you observed in the datasets you studied? Considering that instruments are quite reproductive apart from some glitches leading to NA at random, do you think that imputation should be done ...
written 6 weeks ago by SamGG • 180
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Comment: C: Dealing with NA values from mass spec data using Limma, NA values.
... Many thanks for sharing your views Gordon. If I summarize correctly, your approach applies when one considers NA arising at random whereas my proposal applies when one considers NA arising because of low signals. Weighting is an interesting approach, but playing Evil's advocate, I am wondering if ...
written 6 weeks ago by SamGG • 180
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Comment: C: Dealing with NA values from mass spec data using Limma, NA values.
... Dear Gordon, it's a good news to know you working on Mass Spec data. I think limma is great for such processing after some transformation of the data. Not Missing At Random data is the challenge. From my experience, the data should be first divided by 1e6 or 5e5 prior to transformation with log2 or ...
written 6 weeks ago by SamGG • 180
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Answer: A: flowCore: uneven number of tokens / The last keyword is dropped.
... Hi, This warning arises usually when the file dos not comply to the FCS standard. You could check the compliance with http://bioinformin.cesnet.cz/flowIO/ (flowIO, CLIP, Prague) or https://primitybio.github.io/fcs-validator/ (Zach Bjornson). More on such error in [problems with fcs 3.1 files exporte ...
written 6 weeks ago by SamGG • 180

Latest awards to SamGG

Popular Question 22 months ago, created a question with more than 1,000 views. For How to carry out a gene set analysis using custom gene sets?
Scholar 3.6 years ago, created an answer that has been accepted. For A: samr: understanding scoring line not parallel to diagonal; reproduce example C
Scholar 3.6 years ago, created an answer that has been accepted. For A: Problem with HDF5 and ncdfFlow
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