User: biominer

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biominer10
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European Union
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5 days, 8 hours ago
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2 years, 7 months ago
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Posts by biominer

<prev • 12 results • page 1 of 2 • next >
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Comment: C: Differential drug dosage effect between two genotypes in limma
... I can't thank you enough for your input, James ... that clears up things A LOT for me !!!   ...
written 5 days ago by biominer10
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Comment: C: Differential drug dosage effect between two genotypes in limma
... Thanks again for checking, much appreciated!  One thing I still don't get my head around is the relationship between the contrasts defined above in limma and an interaction term in a standard R linear model. I have an idea what an interaction is in a standard R model where you have two independent ...
written 5 days ago by biominer10
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Comment: C: Differential drug dosage effect between two genotypes in limma
... Another reason why I posted the question originally was that the result of the calculation for the difference of differences didn't look right. There were a lot of genes reported significantly changed which are usually pretty constant in expression across experiments. So perhaps just as a summary of ...
written 5 days ago by biominer10
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Comment: C: Differential drug dosage effect between two genotypes in limma
... Hello James and thanks for your input! I had had a look into this example in the limma userguide and calculated the contrasts as difference of differences as suggested in section 9.5.1 for the two dosage-levels separately. However my example has two (potentially more) levels of rising dosage of the ...
written 5 days ago by biominer10
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Differential drug dosage effect between two genotypes in limma
... I've got an expression data set with a wild type and a knock-down genotype both treated with two different dosages of a drug. I'd like to get the genes that are more effected by treatment (ideally across dosages) in one genotype compared to the other. Since both the genotype and the treatment contr ...
limma linear model model formula dose-response written 6 days ago by biominer10 • updated 6 days ago by James W. MacDonald45k
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limma voom's (and edger's) use of scaling factors
... I am using limma-voom for an RNA-Seq dataset with global down-regulation of gene-expression (experimentally confirmed). On top of that there is also a small set of genes in this dataset that is massively(!) up-regulated. I can't use RLE or TMM normalization because they normalize out the down-regula ...
normalization limma edger limma voom written 12 days ago by biominer10 • updated 12 days ago by Aaron Lun17k
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limma symbols2indices from gmt files versus rdata files
... Hello, I'd like to do an enrichment using romer/roast/camera and my input are HGNC official human gene symbols. For the symbols2indices() function I need a list of vectors for the reference gene sets, either from the rdata files provided by you or generated from the gmt-files from Broad institute. ...
limma roast romer written 23 months ago by biominer10 • updated 23 months ago by Gordon Smyth32k
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Comment: C: DEXSeq exon usage values in result table
... Thanks a lot for your immediate reply! Effect size is exactly what I am aiming for, so I filter for p-value and fold change. I found I might also have to filter for a minimal read count ... or would you say that a significant p-value should already account for sufficient read-coverage? ...
written 2.0 years ago by biominer10
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DEXSeq exon usage values in result table
... In the HTML output of the DEXSeqHTML() function I have figures for both expression as well as exon usage of individual exons. I have also produced a result table using estimateExonFoldChanges() and then DEXSeqResults(). The numbers in the html report graphics and the numbers in the table output ar ...
dexseq exon usage differential exon usage written 2.0 years ago by biominer10 • updated 2.0 years ago by Alejandro Reyes1.5k
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DEXSeq with mutliple experimental conditions - definig contrasts
... I am using DEXSeq in a dataset with a couple of experimental conditions. As I would do in DESeq I had planned to calculate normalization factors, dispersion and the GLM using the whole dataset and then calculate alternative splicing for selected contrasts only (e.g. condition2 versus condition1, co ...
dexseq written 2.6 years ago by biominer10 • updated 2.6 years ago by Alejandro Reyes1.5k

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