User: SamGG
SamGG • 140
- Reputation:
- 140
- Status:
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- Location:
- France
- Last seen:
- 4 weeks, 1 day ago
- Joined:
- 4 years, 1 month ago
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- s***************@inserm.fr
Posts by SamGG
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... Hi Samuel.
I don't have an answer. I already did some test using OMIP018 and this function was OK with the parameters you used. Look at my tests at http://rpubs.com/SamGG/spillover-omip-018 and issue IMHO concerning the row normalization https://github.com/RGLab/flowCore/issues/94
I encouraged you ...
written 7 weeks ago by
SamGG • 140
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... No doubt limma is perfect. GeneAnova does seem to compute a standard ANOVA and does not seem to manage false discovery rate. IMHO, this makes a big difference.
You can increase the FDR threshold up to 20%, but there is chance that the differences in your experiment are not related to the PHENO para ...
written 7 weeks ago by
SamGG • 140
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... Could you check the columns of the design by issuing colnames(design)? I am wondering whether "PHENO" is the correct way to name the column of interest.
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written 7 weeks ago by
SamGG • 140
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... Hi,
I will give you quick answers, letting place for improvements by others more qualified than I am.
1. IIRC, linearize transform data linearly such that minimal value is zero and maximal is one. I always set transformation to FALSE.
2. If export is FCS v2, data are usually compensated and trans ...
written 8 weeks ago by
SamGG • 140
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... Hi ! Short answer: you are trying to estimate nearly as many parameters as samples. The * in the formula means that you are looking for interactions between the factors as well as well the factors independently. In order to estimate the factors without interactions, replace * by +. Long answer: I gu ...
written 8 weeks ago by
SamGG • 140
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... a) the final message might be simply a warning. If you do library(limma), do you get an error? If not, the limma package is correctly installed, but the others packages failed to be updated. Not a big deal if you installed R recently.
b) if you want to install packages at another place, the simples ...
written 9 weeks ago by
SamGG • 140
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... The flowset should consists in the compensation controls plus one unstained sample. Moreover you should set only one value for the stain_match option. I would recommend "ordered" and organize the controls in the order of the channels in the flowset you give to the spillover function. Doing so you ar ...
written 10 weeks ago by
SamGG • 140
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... Oops, I thought the batch id was encoded by the rx suffix. Using the correct batch identifier, I think using PC2 is even more obvious for clustering. Batch variance is clearly taken into account by PC1, and ComBat sounds to be overkill to me. Thanks for your remark.
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written 11 weeks ago by
SamGG • 140
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... Hi,
From a naïve point of view, I would say that all samples but six samples of the first batch have a high background signal that prevents from measuring low levels. You could check that hypothesis by plotting the first 3 controls of batch 1 vs controls of batch 2 or 1. If you got a nice straight ...
written 11 weeks ago by
SamGG • 140
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Comment:
C: GEOquery http:// url error
... As stated by Sean, the easiest solution is to upgrade.
He did some recent changes to fix the problem you mentioned.
...
written 12 weeks ago by
SamGG • 140
Latest awards to SamGG
Scholar
2.6 years ago,
created an answer that has been accepted.
For A: samr: understanding scoring line not parallel to diagonal; reproduce example C
Scholar
2.6 years ago,
created an answer that has been accepted.
For A: Problem with HDF5 and ncdfFlow
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