User: matt.arno

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matt.arno0
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Posts by matt.arno

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Comment: C: Block x Treatment interaction test with DeSeq
... Dear Simon - I know this is a very late follow up - but there is a reason I need to relate directly to this post. I am interested in replicating this (i.e. ~ population + treatment + population:treatment, in my case ~ gender + disease + gender:disease, 22 samples in total (each one from a different ...
written 3.8 years ago by matt.arno0
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Comment: C: goseq analysis - extracting list of my genes which are DE in the enriched GO cat
... Hi Ian and Helen - I tried this bit of code but got an error at the point of  > terms <- stack(lapply(mget(cats, GOTERM, ifnotfound=NA), Term)) Error in stack(lapply(mget(cats, GOTERM, ifnotfound = NA), Term)) :    error in evaluating the argument 'x' in selecting a method for function 'stac ...
written 3.8 years ago by matt.arno0
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Comment: C: Goseq with small numbers of genes: minimum number?
... ...I think I've got the wrong end of the stick with this: the method=sampling means not using the Wallenius method for the null distribution. For some reason I thought this was a background analysis or negative control to compare the real thing to... ...it must be getting late... matt     ...
written 3.8 years ago by matt.arno0
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Goseq with small numbers of genes: minimum number?
... Hi - I have some relatively small genes lists (around 10-20 significant genes (padj<0.05), and tried goseq to look for over represented GO terms and KEGG pathways. I also did the 'sampling' method as a negative control but this gave very similar results to the real test (similar pvalues and terms ...
goseq written 3.8 years ago by matt.arno0
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Comment: C: Can DESeq correlate genes expression patterns with a numerical sample factor?
... just in case you are interested in my outcome with this? (might be helpful for others looking to do same thing)... Firstly, I tried the sva method, followed the code exactly as Michael's guide on the RNAseqGene page, and here is my head(results(dds),4): ranked on pvalue > head(resSva.O, 4) log ...
written 3.8 years ago by matt.arno0
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Comment: C: Can DESeq correlate genes expression patterns with a numerical sample factor?
... thanks - i'll look into that. I wasn't using PCA for batch error correction, just to examine sample relationships. Just to clarify: I don't think this is a batch effect per se, as there were no batches: all samples were processed together. no lane effect as all samples were spread equally across 8 l ...
written 3.8 years ago by matt.arno0
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Can DESeq correlate genes expression patterns with a numerical sample factor?
... Hi - is it possible to correlate gene expression patterns with a linear numerical factor in DESeq? Here's the background: I have used DESeq to analyse gene expression in 40 RNAseq samples; three sample groups.   I have noticed on the PCA that gender is a very strong determinant (=PC1) and one of t ...
deseq deseq2 linear correlation written 3.8 years ago by matt.arno0 • updated 3.8 years ago by Ryan C. Thompson7.3k
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Comment: C: Simple pathway enrichment analysis for gene lists
... Dear Paul - I know a while has elapsed since your post, but I'm trying it out and am stuck at one point. I think the issue I have is inexperience with R/coding rather than a specific problem with this method. Bearing this in mind, would you be able to help? I have installed/loaded KEGGREST etc. l ...
written 3.9 years ago by matt.arno0
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Comment: C: How do I extract the principal components in DESeq2?
... Hi - I wonder if you could let me know how to modify this code and save it as a new function that calls the 2 PCs of interest, e.g. 1 and 2 (default) or 3 and 4 as variables, perhaps>? I guess it's the line: d <- data.frame(PC1 = pca$x[, 1], PC2 = pca$x[, 2], group = group,  where the [,1] ...
written 3.9 years ago by matt.arno0
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Comment: C: DESeq -padj
... Dear Simon - Further to your comments on FDR and padj: does that mean that a frequency histogram of padj is invalid as these values refer to a threshold rather than individual values? What I mean is: a histogram of FDRs would be invalid as each FDR value only applies to the list of genes above it in ...
written 3.9 years ago by matt.arno0

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