User: Adrian Johnson

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Posts by Adrian Johnson

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Leading edge analysis
... Dear group,  I am wondering if there is any leading edge analysis function independent of GSEA available in bioconductor   I have 10 different gene sets. I want to identify and depict genes that can be present in many of the 10 gene sets.  Similar to Leading edge analysis available in standalone ...
enrichment analysis leading edge analysis written 13 months ago by Adrian Johnson330
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GSVA es.obs why range is between -1 and 1
... Dear group and GSVA team,  I am seeing enrichment score (es.obs) for gsva range from -0.9994342  0.9999434.  > range(mresgsva) [1] -0.9994342  0.9999434 why are ES.obs scores ranging from -1 to 1. Is this score similar to correlation coef ? Any help is appreciated and thanks in advance.  mre ...
gsva written 15 months ago by Adrian Johnson330
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GEOQuery - Encoding UTF-8
... Hello: I am trying to download GSE data tables and encountered the following error.  I cannot find a proper solution. Could someone help.    Thanks Adrian     > GSE2034_clindata=getGSEDataTables("GSE2034") No encoding supplied: defaulting to UTF-8. Error in UseMethod("xpathApply") :    no ...
geoquery utf written 15 months ago by Adrian Johnson330
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Answer: A: Common probes between 27K and 450 chip
... Thank you very much.  ...
written 16 months ago by Adrian Johnson330
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Common probes between 27K and 450 chip
... Hello: I am interested in obtaining common probes between 27K and 450 chip. Is there a way I could get the intersection of these two probes. thanks Adrian ...
illimina 450k methylation written 16 months ago by Adrian Johnson330
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test for overlap
... Hi: I am not sure in which forum I have to ask this question - R or bioconductor. I am asking here since it is biology based question. I have two proteins with a domain 'A' that is common to both protein. The domains are 80% identical to each other using a protein alignment. If I assume that if t ...
alignment written 4.2 years ago by Adrian Johnson330
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cummerBund - how to get splicing events
... Hi: In sample 1 (where 4 different conditions were analyzed using cufflinks), using cummberbund, how to get significant number of splicing events? Any other way to do this. Appreciate your help! thanks Adrian ...
written 4.7 years ago by Adrian Johnson330 • updated 4.7 years ago by Valerie Obenchain ♦♦ 6.4k
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Comment: C: cummerbund how to get matrix for csheatmap
... Thank you Valerie and Loyal. That was helpful. Adrian On Tue, Mar 5, 2013 at 11:24 PM, Loyal Goff wrote: > To follow up, there also exists an fpkmMatrix() method to reshape the fpkm results into a feature X condition matrix, e.g.: > > fpkmMatrix(myGenes) > > Cheers, > Loyal > ...
written 4.7 years ago by Adrian Johnson330
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cummerbund how to get matrix for csheatmap
... Hi: I am trying to plot the most significant genes. I have 3 different sample types and 4 replicates each. Could anyone suggest how do I get the matrix of fpkm values that was plotted in csHeatmap function. > diffGeneIDs <- getSig(cuff,level="genes",alpha=0.001) > diffGenes<-getGenes(cu ...
written 4.7 years ago by Adrian Johnson330 • updated 4.7 years ago by Valerie Obenchain ♦♦ 6.4k
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time series expression data
... Hi: Are there any ways or algorithms to carry out a meta-analysis of time series gene expression data sets. I know it is not an appropriate analysis since timepoints may not be comparable across experiments. However if I could choose only comparable time points (Say study1 and study 2 have common ti ...
written 4.9 years ago by Adrian Johnson330

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