User: Darklings

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Darklings0
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Posts by Darklings

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Comment: A: How to access gene IDs associated with GO terms in GOSeq
... I found that if using org.Hs.egENSEMBL will return the GRCh38 ESIDs, while my former analyses used hg19 annotations.  > org.Hs.eg.db OrgDb object: | DBSCHEMAVERSION: 2.1 | Db type: OrgDb | Supporting package: AnnotationDbi | DBSCHEMA: HUMAN_DB | ORGANISM: Homo sapiens | SPECIES: Human | EGSOURC ...
written 4 weeks ago by Darklings0
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How to access gene IDs associated with GO terms in GOSeq
... I did the GO terms enrichment analysis using GOSeq, after that I want to access the esIDs in the significantly enriched terms. I tried to extract esIDs using org.Hs.eg.db and GO.db, according to the vignette and this post. For example using this category GO:0009063. library(org.Hs.eg.db) library( ...
go goseq ensemblid written 4 weeks ago by Darklings0 • updated 4 weeks ago by James W. MacDonald48k
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Comment: C: Get the countsFromAbundance as limma input
... I just drew the logCPM density plot, then I saw some weird lines in both raw & filtered plots (I have highlighted them with blue boxes):  https://drive.google.com/open?id=1qIvW-fiO3MC1QA_0-5putL307Brx7N6h I filtered the data using the filterByExpr() function. Do these lines mean some samples ha ...
written 3 months ago by Darklings0
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Comment: C: Get the countsFromAbundance as limma input
... Hi Smyth, thanks for your suggestion. Actually I tried both limma-trend and limma-voom, they didn't cost too much time. I found that if using limma-trend, the p-values in toptable are much higher and logFC are much smaller than those in limma-voom's. The following is my code: # limma-voom: v0 < ...
written 3 months ago by Darklings0
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Get the countsFromAbundance as limma input
... I am analyzing the TCGA data and doing the differential expression analysis for about 6,000 samples and 20,000 coding genes. I was suggested to use DESeq2 for DE analysis, but the DESeq() takes an extremely long time with 6,000 samples, therefore I would like to use the limma-voom instead. In the t ...
limma deseq2 differential expression tximport written 3 months ago by Darklings0 • updated 3 months ago by Gordon Smyth35k
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Error in ebayes in limma when analyzing GTEx data
... Hi there, I am building a linear model to analyze the expression profiles of cvd and non-cvd subjects. There are 227 samples here.  When fitting the model: design = model.matrix(~ race + age + bmi + gender + batch + cvd + subject) fit = lmFit(voomOutput, design) fit = eBayes(fit) tt  = topTable( ...
limma voom gtex written 8 months ago by Darklings0

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