User: salamandra

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salamandra0
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Posts by salamandra

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Comment: C: DEseq2: Is vst/rlog transformation applied to raw counts or normalised counts?
... Thanks. So, counts are not scalled by row/mean gene expression (unlike the normalized counts for differential expression analysis)? Is it ok to subtract rlog values by log of mean expression of each gene before doing dendrogram, then? ...
written 7 months ago by salamandra0
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deseq2: use blind=T or blind=F when find gene groups?
... Hi, I'm using reduced model to get genes that vary over different conditions and using degPaterns() to split those genes into groups according to their expression pattern (code bellow). What want to know is in this case, should we use parameter blind=T or blind=F in rlog() ? Table <- data.fram ...
deseq2 rlog transformation written 7 months ago by salamandra0 • updated 7 months ago by Michael Love25k
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Comment: C: DEseq2: Is vst/rlog transformation applied to raw counts or normalised counts?
... Honestly even after reading manual pages I don't understand cause of the statistical terms. I'm trying to learn more on that area though. So, it means vst/rlog 'correct' for library size, but still dind't get if they correct for average gene expression across samples. And also, in this case should ...
written 7 months ago by salamandra0
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DESeq2: interaction term
... If we look at the example of Deseq2 vignette on interaction terms: https://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#interactions Table sampleName fileName genotype condition group 1 AI_s1 A1_ATCACG_counts I A AI 2 AI_s2 A2_T ...
deseq2 written 7 months ago by salamandra0
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DEseq2: Is vst/rlog transformation applied to raw counts or normalised counts?
... Hi, When applying vst or rlog transformations to rna-seq data to latter on visualize it in a heatmap with dendrograms, is vst/rlog applied to raw counts or instead to normalized counts when we do assay(rlog(ddsHTSeq, blind=F)) ? By normalized counts I mean corrected with scaling factor calculated ...
deseq2 rlog transformation vst written 7 months ago by salamandra0 • updated 7 months ago by Wolfgang Huber13k
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draw.pairwise.venn: Misplaced line connecting external area label
... Hi, in venn diagram here the line connecting external intersection area label to its anchor point is misplaced, does anyone know what parameter of the function draw.pairwise.venn corrects for this? png(paste0(dir,condition[j],'.Human.MEF',timecorr[i], '_vennNumber.png'), res = 300, height = 20*30 ...
venndiagram written 9 months ago by salamandra0
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Question: Enrichment heatmap - GOstats package of R
... I wanted to build a heatmap with different sets of genes as columns and GO BP terms as rows. The intensity of the colour of each cell in the heatmap would represent the p-value. I started by using hyperGTest of package GOstats to calculate p-value for different GO terms. I selected p-value cutoff a ...
gostats p-value written 2.1 years ago by salamandra0
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Comment: C: Visualizing GOstats HyperGTest results
... When I did what you suggest it didn't return all GO terms, as the number of GO terms is varying with the gene set. Here is an example: A <- c("86", "51412", "192669", "8289", "57492", "83858", "10533", "10538", "54880", "1230", "947", "79577", "55038", "64866", "1017", "1026", "1063", "1105", ...
written 2.1 years ago by salamandra0
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What are out-of-bound ranges? Is it necessary to get rid of them?
... With the function: overlaps.anno <- annotatePeakInBatch(overlaps, AnnotationData=annoData, output="nearestBiDirectionalPromoters",bindingRegion=c(-2000, 500)) got this warning message: Annotate peaks by annoPeaks, see ?annoPeaks for details. maxgap will be ignored. Warning messages: 1: In v ...
chippeakanno R written 2.4 years ago by salamandra0

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Popular Question 7 months ago, created a question with more than 1,000 views. For What are out-of-bound ranges? Is it necessary to get rid of them?

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