User: andrea.rau

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andrea.rau60
Reputation:
60
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Location:
INRA / Jouy en Josas, France
Website:
http://www.andrea-rau....
Twitter:
andreamrau
Last seen:
8 months, 1 week ago
Joined:
5 years ago
Email:
a*********@inra.fr

Statistician + author of some R (ebdbNet, HTSCluster, HTSDiff) & Bioconductor (HTSFilter, coseq) packages

Posts by andrea.rau

<prev • 11 results • page 1 of 2 • next >
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Answer: A: Coseq error with DESeq2 object: Error in "normFactors"
... Once the `model` and `transformation` arguments of coseq were correctly specified, the problem here arose from the fact that the data were processed using tximport prior to the DESeq2 analysis, which meant that no normalization size factors were available in the `DESeqDataSet` object for coseq to us ...
written 8 months ago by andrea.rau60
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Comment: C: Coseq error with DESeq2 object: Error in "normFactors"
... Wonderful, I'm glad it worked! And yes you're right, the `which` index will indeed only consider the genes significant at `padj < 0.05` from the LRT test in my above code. I'm going to add an answer below to close out this question, and I will try to add something in the coseq documentation to i ...
written 8 months ago by andrea.rau60
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Comment: C: Coseq error with DESeq2 object: Error in "normFactors"
... Thanks for the extra detail -- I think I know what's going on here. Because the data here were processed using tximport prior to the differential analysis, the `DESeqDataSet` object does not include any normalization factors that can be accessed via `sizeFactors(dds)` (which is how coseq attempts to ...
written 8 months ago by andrea.rau60
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Comment: C: Coseq error with DESeq2 object: Error in "normFactors"
... Thanks for double-checking your parameters. Is there any way you could send a fully reproducible example? I'm having trouble reproducing your error. When you run the analogous example from the vignette, do you get the same error you're seeing with your own data? ``` library(coseq) library(DESeq2) ...
written 8 months ago by andrea.rau60
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Comment: C: Coseq error with DESeq2 object: Error in "normFactors"
... Hi @varunorama, I wanted to clarify the specific analysis you're trying to perform here: - You've specified `normFactors = "none"`, which means that the clustering analysis will *not* make use of the library size normalization factors that were calculated by DESeq2. I would strongly recommend that ...
written 8 months ago by andrea.rau60
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Answer: A: function meaning(on.index <- which(filter$on == 1))
... In this code, the HTSFilter package is being used to filter the data (contained in the cds object) to remove genes with relatively low counts across samples using a data-driven filtering threshold. The HTSFilter function returns both the filtered data themselves (contained in filter$filteredData, wh ...
written 2.3 years ago by andrea.rau60
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Comment: C: Running HTSFilter in paralell
... After a longer delay than expected (my apologies!), HTSFilter now implements (as of Bioconductor 3.4, version 1.14.0) the option for parallel calculations through the BiocParallel package. There are now two additional optional arguments in calls to HTSFilter: parallel (TRUE/FALSE) and BPPARAM to spe ...
written 3.0 years ago by andrea.rau60
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Answer: A: Error when trying to run HTSFilter
... If you have one condition that has a single replicate, I would think there are two options you could try: 1) For the purposes of filtering via HTSFilter, you could just assimilate that singleton sample with the replicates from the closest/most similar condition (i.e., just in the filtering step, no ...
written 3.0 years ago by andrea.rau60
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Comment: C: Error when trying to run HTSFilter
... Hi and thanks for your question. I think I'll need some additional information, as I'm not currently able to replicate your error. In particular, could you send me a minimal reproducible example that throws the same error that you're seeing so that I can work off that? Also, what version of HTSFilte ...
written 3.0 years ago by andrea.rau60
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Answer: A: Running HTSFilter in paralell
... Ok, I will work on adding the possibility of parallel calculations to HTSFilter. It may take me a couple of weeks to get around to it, but I will let you know when it is ready for testing in the development version. Thanks again for the feedback! Best, Andrea ...
written 3.8 years ago by andrea.rau60

Latest awards to andrea.rau

Scholar 3.8 years ago, created an answer that has been accepted. For A: Error when trying to run HTSFilter
Autobiographer 5.0 years ago, has more than 80 characters in the information field of the user's profile.

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