User: sup230

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sup23010
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Posts by sup230

<prev • 13 results • page 1 of 2 • next >
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GSEA using clusterprofileR
... Hi,  I am wondering how the result of GSEA using cluster profiler is different from that of GSEA GUI java application. I initially used GSEA GUI desktop application and tried clusterprofileR package in R using gseKEGG function. I assigned latest kegg database available online and pvalue cutoff of 0 ...
clusterprofiler gsea written 5 days ago by sup23010 • updated 5 days ago by assaron130
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Error downloading the package
... Hi,  I am trying to download TCGA biolinks and for some reason I keep getting error message I don't understand what the problem is because I have used it to download data from TCGA with no problem just a few weeks ago. The warning I am getting is this: Error: package or namespace load failed for ...
download tcga tcgabiolinks written 4 weeks ago by sup23010 • updated 4 weeks ago by James W. MacDonald44k
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design contrast in limma package for microarray expression data
... Hi,  I just wanted to get confirmation that the following code would get me the result I wanted. So I am interested in getting the list of differential expressed genes between two groups between seizure YES and seizure NO. The expression set is the microarray data and seizure information is in the ...
limma design and contrast matrix differential gene expression written 8 weeks ago by sup23010 • updated 8 weeks ago by Aaron Lun16k
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Comment: C: Can't find gene list for KEGG genesets
... Thank you- This worked! Could you also help me with matching the KEGG gene IDs to either gene symbols, Entrez ID, or Ensembl IDs? ...
written 9 weeks ago by sup23010
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Can't find gene list for KEGG genesets
... Hi, I used both gage package in R and GSEA software for KEGG pathway analysis and since the 2 tools have different algorithms, I got slightly different results in the list of genesets. I was able to find the genes in each gene set from GSEA from their website, but I don't seem to find the gene list ...
kegg geneset gage package genelist written 9 weeks ago by sup23010 • updated 9 weeks ago by Gordon Smyth32k
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Comment: C: log2 fold change calculation for DE gene analysis
... Yes! This sounds like a much more efficient and right way. I have a couple followup questions though.  When I calculate the mean and standard deviation for the control group, I would only include the genes in a particular gene set, because higher z-score would still mean that gene set is more enric ...
written 10 weeks ago by sup23010
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log2 fold change calculation for DE gene analysis
... Hi,  I have questions that are not a part of typical RNAseq work flow so I would like lots of your input/help! I used DESeq2 to get the full list of DEgenes with their respective log2fc between the two phenotype groups in my data. The metadata are TCGA-LGG samples and I am interested in phenotype ...
deseq2 log2fc l2fc written 10 weeks ago by sup23010 • updated 10 weeks ago by Michael Love14k
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DESeq2 - GAGE workflow
... I have some confusion about GAGE workflow. I understand GAGE is a type of functional class scoring tools with no preset cutoff used to identify significant genes. But I have seen several workflow/model scripts where they used the output from DESeq2 which is selected based on p-adjusted value of 0.05 ...
deseq2 gage package written 11 weeks ago by sup23010
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Comment: C: DESeq function taking too long
... Can you elaborate briefly how different the two methods are between DESeq and limma-voom?  ...
written 12 weeks ago by sup23010
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Comment: C: DESeq function taking too long
... Thanks for the clarification!  The resource monitor shows 79% used physical memory: 6393 MB in use and 1653 MB available. The number of hard faults as listed under processes is 0 but on the graph to the right side, I see some peaks come and go. Any suggestion of soluiton if this seems to be the cau ...
written 12 weeks ago by sup23010

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