User: jackipchiho

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jackipchiho10
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New User
Location:
Hong Kong
Last seen:
4 years, 1 month ago
Joined:
4 years, 3 months ago
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j**********@hotmail.com

Posts by jackipchiho

<prev • 11 results • page 1 of 2 • next >
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How to use REVIGO to remove redundant GO term
... Hi ALL, I have obtained a long list of GO terms in GOSeq. First, I would like to ask did GOSeq result can be used for analysis in REVIGO? if yes, should I input p-value or corrected p-value (method="BH") and what is the cutoff value? If I separate BP, CC and MF to perform REVIGO, will it affect the ...
goseq revigo written 4.2 years ago by jackipchiho10
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Detail of GAGE's esset.grp function
... HI ALL, I have run GAGE to find out the enriched GO and KEGG term between control and chemical treatment for non-model species. In some comparison, some enrichment terms/pathways contained some common genes, then I tried to use "esset.grp" to extract the non-redundant pathways.  However, I am not ...
gage written 4.2 years ago by jackipchiho10
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Comment: C: About GOSeq GO and KEGG enrichment analysis
... Thanks Keith, yes, I also read that paper ytd. I will run the analysis again today ...
written 4.2 years ago by jackipchiho10
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Answer: A: About GOSeq GO and KEGG enrichment analysis
... Dear Gordon, Thanks for your explanation.  If the nonannotated DEGs will affect the overall results, should I remove them? or should I separate the up or down regulated genes to run GOseq again? as all DEGs only marked with "1" in DEG input file. For p-value, I tried to run the analysis with sepa ...
written 4.2 years ago by jackipchiho10
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About GOSeq GO and KEGG enrichment analysis
... HI ALL, I am working on non model species, and now I want to use GOseq to perform GO and KEGG enrichment analysis. I have found a list of DEGs using DESeq2, FDR <= 0.05, |log2FC| => 1. However, some of those DEGs (say 50%) haven't associated with any GO and KEGG annotation. Will it affect th ...
goseq written 4.2 years ago by jackipchiho10
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How to fully use the list of DEGs in non model species?
... Hi ALL, I am a beginner of RNAseq study. I am working on the transcriptome of non model species, mussel and snail. Now I have done exposure experiments and RNAseq to determine the toxicity mechanism. Now I have performed DESeq2 and EBSeq, I have a list of DEGs. As the molecular information of my t ...
rnaseq gage deseq2 ebseq written 4.3 years ago by jackipchiho10
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Comment: C: Urgent: Do GAGE applicable for non model species?
... Thanks Weijun, I have revised the code: >list.files() "Rckegg.gs.gmt"    "Rcg30.txt" >Rckegg.gs <- readList("Rckegg.gs.gmt") >head(Rckegg.gs[1:2]) $Ko00010   [1] "comp10418997_c0" "comp11135183_c0" "comp11547_c0" ....... $Ko00020  [1] "comp106429_c0"   "comp11438380_c0" "comp118524 ...
written 4.3 years ago by jackipchiho10
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Answer: A: Urgent: Do GAGE applicable for non model species?
... I tried the following way to do the analysis based on my own kegg gene set data: > filename=system.file("extdata/Rckegg.gmt", package = "gage") > Rckegg.gs=readList(filename) > data(Rc_30BgF) > Cg=1:3 > Bg=4:6 > Rc.kegg.unp <- gage(Rc_30BgF, gsets = Rckegg.gs, ref = Cg, samp = ...
written 4.3 years ago by jackipchiho10
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Answer: A: Urgent: Do GAGE applicable for non model species?
... I have created a kegg gene set (Rc_kegg.txt) based on my own annotation data: Ko00010    Glycolysis / Gluconeogenesis    comp10418997_c0    comp11135183_c0    comp11547_c0    comp124788_c0 ......    Ko00020    Citrate cycle (TCA cycle)    comp106429_c0    comp11438380_c0    comp11852469_c0    comp ...
written 4.3 years ago by jackipchiho10
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Urgent: Do GAGE applicable for non model species?
... Hi ALL, Since I am working on non model species green mussel and intertidal whelk, I would like to know can I use GAGE to perform gene set analysis for control and chemical treatment groups (n=2 / n=3)? If yes, how can I do it? I have done de novo transcriptome and worked out the KEGG (Ko and K nu ...
gage written 4.3 years ago by jackipchiho10 • updated 4.3 years ago by amywingsze0

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