User: dorothy.jrobbert

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Posts by dorothy.jrobbert

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Comment: C: How to convert data frame obtained with enrichPathway back to an enrichPathway r
... Yes, my x12 in the code is the enrichment result! ...
written 6 months ago by dorothy.jrobbert20
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Comment: C: How to convert data frame obtained with enrichPathway back to an enrichPathway r
... It worked when I specified the gene list in the emapplot and cnetplot function itself like: id_list<-c("R-MMU-512988 ","R-MMU-451927 ","R-MMU-912526 ") cnetplot(x12,ID=id_list,foldChange=lfc12,vertex.label.cex = 1.2) Thanks for your help! ...
written 6 months ago by dorothy.jrobbert20
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Comment: C: How to convert data frame obtained with enrichPathway back to an enrichPathway r
... I tried this where x@result was my enrichResult. The command worked. But the emapplot and cnetplot function show the same error " Error in (function (classes, fdef, mtable)  :    unable to find an inherited method for function ‘emapplot’ for signature ‘"data.frame"’ It looks like the command outpu ...
written 6 months ago by dorothy.jrobbert20
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How to convert data frame obtained with enrichPathway back to an enrichPathway result after editing/subsetting?
... I have a list of 291 genes which I had enriched for pathway analysis using the "enrichPathway" function of ReactomePA. I then visualised the enrichment as pathways using the dotplot, emapplot and cnetplot functions.  In the emapplot visualisation, I get broadly two distinct connected sets of pathwa ...
reactomepa written 6 months ago by dorothy.jrobbert20 • updated 6 months ago by Guangchuang Yu1.1k
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Evaluating Hub genes in WGCNA and role of using Signed network
... I have a dataset in which I study the effects of a demethylating agent. I have 16 control untreated samples and 16 treated samples (with the demethylating agent) of moue haematopoetic stem cells. RNA-Seq data was obtained for all 32 samples. I used DESEq2 package to calculate DE. I intended to obtai ...
rnaseq wgcna written 10 months ago by dorothy.jrobbert20
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Solving error for error of factors
... Hello, I have a very large dataset which I downloaded from TCGA for pancreatic cancer. It has one normal sample but 184 patient samples. So, It has 186 columns (no technical replicates) and 20500 rows for all the genes. I am trying to get log2fold change data from this using deseq2. To begin my ana ...
cancer deseq2 R written 21 months ago by dorothy.jrobbert20 • updated 21 months ago by Michael Love24k
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Comment: C: Matching columns to sample names
... Hello, I have a very large dataset which I downloaded from TCGA for pancreatic cancer. It has one normal sample but 184 patient samples. So, It has 186 columns (no technical replicates) and 20500 rows for all the genes. I am trying to get log2fold change data from this using deseq2. To begin my ana ...
written 21 months ago by dorothy.jrobbert20

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