User: Simone

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Simone170
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Posts by Simone

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Comment: C: QC and normalization of 450K data from CSVs instead of IDATs
... Thanks for your reply, Yuan. I know that ChAMP does not need an MethyLumiSet and that I can run norm_pbc <- champ.norm(beta=mybeta, method="PBC", arraytype="450K") on just the beta values. The same for BMIQ. But for FunctionNormalization, I would require an rgSet, and for SWAN normalization b ...
written 11 months ago by Simone170
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QC and normalization of 450K data from CSVs instead of IDATs
... Hello, I have got some 450K data in CSV format, containing the following information (column names):   CSV file 1: SampleN.AVG_Beta, SampleN.Intensity, SampleN.Signal_A, SampleN.Signal_B CSV file 2: SampleN.Signal_Red, SampleN.Signal_Grn, SampleN.Pval CSV file 3: SampleID, Sample_Well, Sample_pl ...
normalization minfi champ 450k csv written 11 months ago by Simone170 • updated 11 months ago by Yuan Tian90
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Test for differential variability with missMethyl (DiffVar) using block design
... Hello, I would like to test for differential methylation variability using missMethyl, but with a block design to take sample pairs/quartets into account. If I wanted to test for differential (mean) methylation with my experimental design, I would use a code like this for example: design <- mo ...
limma block design matrix missmethyl diffvar written 23 months ago by Simone170 • updated 12 months ago by lhuang730
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Answer: A: IlluminaHumanMethylation450k.db installation error
... I 'solved' it by commenting the code calling .Defunct # if(interactive()){ # .Defunct(new=c(paste0('FDb.InfiniumMethylation.hg', c(19, 18)), # 'mapToGenome() function in minfi or methylumi')) # } Simone ...
written 3.4 years ago by Simone170
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IlluminaHumanMethylation450k.db installation error
... Hello, I am trying to install IlluminaHumanMethylation450k.db but can't manage to do so: Error : .onLoad failed in loadNamespace() for 'IlluminaHumanMethylation450k.db', details: call: NULL error: 'fun' is defunct. Use 'FDb.InfiniumMethylation.hg19' instead. Use 'FDb.InfiniumMethylation.hg18' ...
illuminahumanmethylation450k.db written 3.4 years ago by Simone170 • updated 3.4 years ago by Dan Tenenbaum8.2k
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Comment: C: Perform limma on a subset of genes of interest
... Yes, you understood correctly. I was already suspecting that the independence you wrote about was more of a technical nature regarding the way the p-values are obtained, nevertheless I wanted to be sure, so thank you very much for the further clarification and the helpful discussion. ...
written 4.5 years ago by Simone170
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Comment: C: Perform limma on a subset of genes of interest
... Thank you for the explanation, this is very helpful. Actually the subset of interest in my case is not really independent of the contrast of interest, because the contrast itself is exactly the same as the one used for defining the subset of genes, just on a different dataset of biologically differe ...
written 4.5 years ago by Simone170
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Answer: A: Perform limma on a subset of genes of interest
... Okay, I missed that question (and answer), sorry! So actually the answer is it does not really make sense to perform limma on a subset of genes, or better said it is not a good way to do so, and the filtering should be done after obtaining the results by limma. This is what I imagined. Nevertheless ...
written 4.5 years ago by Simone170
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Perform limma on a subset of genes of interest
... Hello! I've got a small question regarding limma and couldn't find a direct answer anywhere: Does it make sense to perform limma on only a subset of genes? An example: I am only interested in if there are differences in gene expression between the groups of interest in 700 previously defined genes ...
limma written 4.5 years ago by Simone170
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DEXSeq design formula
... Hello! Just a quick question regarding DEXSeq: I have more variables in my experiment (9 samples), i.e. 3 different celltypes (variable of interest) taken from 4 different patients. To take into account when samples come from the same patient I included an additional factor to the sampleData table ...
written 5.0 years ago by Simone170 • updated 5.0 years ago by Alejandro Reyes1.6k

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Popular Question 23 months ago, created a question with more than 1,000 views. For Perform limma on a subset of genes of interest

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