User: bikash2510

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bikash251030
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Posts by bikash2510

<prev • 31 results • page 1 of 4 • next >
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Meta Analysis Of GEO DataSet
... I have to perform a meta-analysis of 10 different expression profile from GEO. Some of the datasets in GEO are with different GPL ID. How can I compare these datasets with different GPL? And I have to find the common gene and there fold change values among these 10 data. So, is there any good packa ...
R metaanalysis microarray rna-seq written 8 months ago by bikash251030
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Comment: C: Enrichpathway In ReactomePA.
... But I am not getting the result as you mentioned here. Please, could you tell me how to do that? And I have to reduce my P-value to 0.01 to get significant pathways. ...
written 8 months ago by bikash251030
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(Closed) Enrichpathway In ReactomePA.
... When I am trying to do enrichpathway in ReactomePA package, I am getting zero observation. No entrezid is mapped. > gene<-c("64240", "6296", "196883", "153", "155", "4299", "2334", "79026", "9495", "1109", "23294", "50636", "343", "394", "50649", "23204", "728619", "4 ...
R reactomepa written 8 months ago by bikash251030 • updated 8 months ago by RamRS19k
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Comment: C: clusterProfiler (enrichKEGG) error
... Some entrezid can't be mapped by clusterprofiller e.g- 4057(LTF),4856(NOV),56603(CYP26B1),6424(SFRP4), I am unable to get what wrong with clusterprofiller. ...
written 8 months ago by bikash251030
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[OP Inactive] clusterProfiler (enrichKEGG) error
... Getting error still after using correct entrezid for BPM4 gene. > x="652" > kk <- enrichKEGG(gene = x, + organism = 'hsa', + pvalueCutoff = 0.05) --> No gene can be mapped.... --> Expected input gene ID: 2194,2271,126,54 ...
guangchuang yu kegg clusterprofiler written 8 months ago by bikash251030 • updated 8 months ago by RamRS19k
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Comment: C: ClusterProfiler Ontology Bar plotting
... Is there any way to plot only specific description(8-10 description) in bar plot. I had read your pdf but didn't found command for the same. ...
written 8 months ago by bikash251030
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Comment: C: enrichment of gene set with enrichR
... Thanks for your suggestion, I have found out the answer for following errors, self-effort matters some time :) ...
written 8 months ago by bikash251030
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Comment: C: enrichment of gene set with enrichR
... If I had enough time to search and learn various tutorial than I could have done it previously, anyone knows the answer then please tell me. ...
written 8 months ago by bikash251030
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Comment: C: enrichment of gene set with enrichR
... If I had an Entrez id than how to convert into vector form in text format. In the above query i had used chrachter form but when i am using it in numeric form it showing error. my_genes <- c("11171", "8243", "112464", "2194", "9318", "79026", "1654", "65003", "6240", "3476", "6238", "3836", "4 ...
written 8 months ago by bikash251030
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Comment: C: Enrichment of gene set with enrichR
... I am not getting any function regarding box plot, dot plot i enrichR. ...
written 8 months ago by bikash251030

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