User: cronanz

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cronanz0
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Posts by cronanz

<prev • 10 results • page 1 of 1 • next >
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edgeR: Strange volcano plot
... Dear all, I have a scRNA-seq data (plate-based) and to identify differentially expressed genes between clusters, I have made use of edgeR. The input data was expected counts from RSEM and the example workflow is as follows: all_edger <- DGEList(counts=all_expc,group=groups) all_edger &l ...
edger dgea scrna-seq written 10 weeks ago by cronanz0 • updated 10 weeks ago by Aaron Lun24k
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kegga() p-value calculated differently in different edgeR versions
... Hi, I was wondering whether anyone could shed light on this discrepancy I observed between two different edgeR versions. I used a version 3.12.1 of edgeR and did all my gene set enrichment analysis with it, but recently I updated the edgeR version to 3.18 and realised that the p-values that were g ...
edger kegga written 2.1 years ago by cronanz0 • updated 2.1 years ago by Gordon Smyth37k
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Adjusting p-values from goana() output
... Hi, I am trying to perform benjamini-hochberg adjustment for the p-values obtained from running goana(). I am wondering which approach is appropriate: 1) get all GO terms with p-values < 1 and adjust them altogether. 2) get all GO terms with p-values < 0.1 (or 0.05) and adjust them altogether ...
limma edger written 2.3 years ago by cronanz0 • updated 2.3 years ago by Aaron Lun24k
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Comment: C: Strange output from goana()
... That makes sense. Thank you always for your detailed response ...
written 2.4 years ago by cronanz0
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Comment: C: Strange output from goana()
... Turns out I got the numbers wrong for the comments I made below. The output is: -1   990 0  10586 1    677 So the upregulated genes are indeed more than the downregulated genes. I suppose this makes the output I got above sense? Apologies for the confusion. ...
written 2.4 years ago by cronanz0
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Comment: C: Strange output from goana()
... Thank you Aaron for your answer. Well if that's the case, that's a big difference in p.values I'm seeing here. I know that it would be prudent to gauge the significance with p.value alone, but given that the above comparison had 70 genes difference between up- and down-regulated genes (more up-regu ...
written 2.4 years ago by cronanz0
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Strange output from goana()
... Dear everyone, I have been using goana() from edgeR to perform GO enrichment analysis on my list of DE genes and I'm puzzled by the results. My code to get the output is as follows: design <- model.matrix(~condition) disp <- estimateDisp(y, design, robust=TRUE) fit <- glmFit(disp, desi ...
edger goana written 2.4 years ago by cronanz0 • updated 2.4 years ago by Gordon Smyth37k
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Comment: C: Including novel transcripts and antisense into differential gene expression anal
... Thank you. While we are on the subject of normalization, I would like to get your opinion on the usage of entrez ids.  This is partly because entrez ids are required for some of downstream analyses in edger such as goana() or kegga(). Because some of the genes (regardless of the organisms they come ...
written 2.5 years ago by cronanz0
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Comment: C: Including novel transcripts and antisense into differential gene expression anal
... Thank you for your comprehensive answer. I am working on a relatively unexplored genome/transcriptome of an organism so I would probably take the same approach for antisense transcripts as the novel transcripts. The antisense transcripts here are not annotated. But I would take your advice and uti ...
written 2.5 years ago by cronanz0
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Including novel transcripts and antisense into differential gene expression analysis
... Dear all, I have a set of RNA-seq data that I performed differential gene expression analysis using edgeR with known annotations taken from a database. After completing this, I decided to set off identifying novel transcripts (novel ncRNAs) and antisense transcripts. It is my intention to quantify ...
rnaseq edger written 2.5 years ago by cronanz0 • updated 2.5 years ago by Aaron Lun24k

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