User: Kim

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Posts by Kim

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Comment: C: Extracting gene symbols from gene assignments in exon array data
... Hi Russ I tried this command and it works. Thank you :) for (i in 1:11005) { Gene_symbol[i] <- strsplit(full_table$gene_assignment, " // ")[[i]][2] } ...
written 4 days ago by Kim0
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Comment: C: Extracting gene symbols from gene assignments in exon array data
... Yes I'm trying to use strsplit but this function works with vector and the "gene assignment" data type is factor so it makes the work not straightforward. ...
written 6 days ago by Kim0
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Extracting gene symbols from gene assignments in exon array data
... Hello everyone I'm working on gene expression data from a human exon array. I want to have a column of gene symbols but the only column giving me that information is "gene assignment" and the information looks like this. NM_001156474 // CCDC81 // coiled-coil domain containing 81 // 11q14.2 // ...
gene symbol exon microarray gene assignment written 6 days ago by Kim0 • updated 6 days ago by Pierre Lindenbaum122k
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Comment: C: Access to analysis to GEO dataset
... Hello Genomax. Thank you for checking that and sorry for replying late. I read your answer and tried to figure out my problem before getting back to you. I can also access the dataset and pull up GEO2R interface, the problem just begins with the analysis. I thought it's my connection issue as it wor ...
written 10 days ago by Kim0
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Comment: C: Export tables of overlapping genes when using GOVenn
... Thank you very much. It's not very straightforward but I can get the table now ...
written 15 days ago by Kim0
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Access to analysis to GEO dataset
... I need the dataset GSE14098 for my project. I could access the database and analyzed it with GEO2R several times before but now I can only access it, not able to use it with GEO2R anymore. When I check Value Distribution, the message is: "The requested page has restricted access! https://ibb.co/C6P ...
geo restricted access parsing error geo2r written 18 days ago by Kim0
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Export tables of overlapping genes when using GOVenn
... Hello everyone I'm using GOVenn in RStudio to find overlapping differentially expressed genes between datasets. My command: GOVenn(dt1, dt2, d3, title = "Overexperessed genes", label = c("CPC vs CPP", "CPC vs aCPP", "aCPP vs CPP)), plot = F) The result is a nice Venn diagram and tables of overl ...
overlapping genes govenn written 20 days ago by Kim0
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Answer: A: Group definition and logFC calculation in GEO2R
... I also emailed GEO2R team and they've just replied. For anyone who has the same question: "The first group that is named in the 'Define groups' drop-down menu becomes the denominator in logFC, and the second group that is named becomes the numerator. The background pink/blue colors are not importan ...
written 22 days ago by Kim0
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Comment: C: Group definition and logFC calculation in GEO2R
... Hi Kevin Thank you for your comment. I agree that what we choose as numerator and denominator are up to our decision. I'm just confused as GEO2R always take Pink/ Blue (control/ treatment) while some people say it's always treatment/ control. But it's useful to know there's no fixed rule on log2FC ...
written 23 days ago by Kim0
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Group definition and logFC calculation in GEO2R
... Hello everyone I'm learning to analyze GEO data and using GEO2R is the most straightforward to me, but I'm having problem understanding how GEO2R (or limma) calculate the logFC. I read this link [https://wiki.bits.vib.be/index.php/Analyze_GEO_data_with_GEO2R][1] and noticed this: "First define t ...
group definition geo2r logfc written 24 days ago by Kim0

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