User: jan.soderman

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Posts by jan.soderman

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Comment: C: A contrast with four simultaneous conditions for DESeq2?
... Hi Michael, Thanks for your reply. I have a follow-up question. First, however, I will comment on the reasons for switching among three packages. New to RNA-seq analysis and without a strong preference based on literature I started out with limma. However, I also wanted to explore the workflow of o ...
written 6 weeks ago by jan.soderman0
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A contrast with four simultaneous conditions for DESeq2?
... Hi, To identify genes that respond differently to inflammation in females and males (with ulcerative colitis) I have set up the following contrast using makeContrasts of the limma package, and analyzed it using limma and edgeR: (UlcerativeColitis.Inflamed.Male-UlcerativeColitis.notInflamed.Male)-(U ...
deseq2 contrast results written 6 weeks ago by jan.soderman0 • updated 6 weeks ago by Michael Love19k
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Moving around nodes using emapplot {enrichplot} or enrichMap {DOSE}
... Hi, I get overlapping text labels in the enrichment map produced by emapplot {enrichplot}. Is there a way to move around the nodes in order to avoid this? If not, is there a way to still use enrichMap {DOSE} and the “fixed = FALSE” parameter? Since I moved to Bioconductor 3.7 enrichMap only result ...
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Remove highly similar terms from a GO gene set enrichment analysis
... Hi, Can you please suggest a method for removing highly similar GO terms from the gseaResult object produced by the gseGO function of the clusterProfiler package? When conducting an GO over-representation analysis using the enrichGO function of the same packge there is a simplify function for remo ...
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Error using gosummaries (GOsummaries) on small log2 fold change values
... Hi, I?m using the gosummaries() function on an eBayes() MArrayLM object. All is well down to lfc = log2(1.35), using the following expression: GOsum1 <- gosummaries(efit, p.value = 0.05, lfc = log2(1.35), go_branches = c("BP"), min_set_size = 5, max_set_size = 1000, adjust.method = "fdr", exp = ...
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Comment: C: Reference for edge and node properties suitable for enrichMap{DOSE}
... I do not understand how a reference to ggplot2 will help me understand the basis for the edge width, node size and node color. Could you please clarify your answer, while waiting for a release with an explanatory legend? Sincerely/ Jan ...
written 6 months ago by jan.soderman0
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Reference for edge and node properties suitable for enrichMap{DOSE}
... Hi, I have used the enrichMap() function of the DOSE package to visualize enrichment results from the enrichPathway() function of the ReactomePA package. I assume that edge line thickness represent the overlap between connected nodes, that node color represent the significance of the enrichment and ...
dose reactomepa enrichmap enrichpathway written 6 months ago by jan.soderman0 • updated 6 months ago by Guangchuang Yu1.0k
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failed ToPASeq / igraph installation: file present, but not found
... Hi, As root, I have tried to install the package 'ToPASeq' (or only the dependency 'igraph') with an error telling me that "libiconv.so.2: cannot open shared object file: No such file or directory" (see below). Using the Linux command: locate libiconv.so.2 I can see that the file exist under the f ...
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Comment: C: Rsubread function buildindex cannot handle the GRCh38.p7 reference from NCBI
... Many thanks for your help James. Using your supplied link to the the latest version of the assembled human genome, I have now successfully indexed the sequence using the buildindex() function of the Rsubread package. Clearly I did not know my way around the NCBI web-site, but have now discovered the ...
written 21 months ago by jan.soderman0
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Rsubread function buildindex cannot handle the GRCh38.p7 reference from NCBI
... Hi, I have tried to use the buildindex() function of the Rsubread package in conjuction with the human GRCh38.p7 reference sequence from NCBI, but get the following error: Check the integrity of provided reference sequences ...                    || ERROR: repeated chromosome name 'gi' is observed ...
rsubread ncbi grch38 hg38 written 22 months ago by jan.soderman0 • updated 21 months ago by Wei Shi2.9k

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