User: cagdas

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cagdas10
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Posts by cagdas

<prev • 12 results • page 1 of 2 • next >
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Comment: C: Remove duplicate genes with lower significance in microarray data analysis
... Hi banerjeeshayantan, I have same problem. Did you fix it and how? Thanks ...
written 9 weeks ago by cagdas10
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Comment: C: remove multiple gene symbols in the affymetrix platform
... Hi Kevin, How can I use limma:avereps for following codes? # Differential expression analysis with limma library(Biobase) library(GEOquery) library(limma) # load series and platform data from GEO gset <- getGEO("GSE60371", GSEMatrix =TRUE, AnnotGPL=FALSE) if (len ...
written 11 weeks ago by cagdas10
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which expression levels should I choose in microarray?
... Hi, I am looking for genes that have altered expression levels. When I use GEO database, I find multiple results for same gene within one dataset. Which of them should I use? If I choose their average or highest value, how can I filter them? Thanks for your help ...
microarray written 11 weeks ago by cagdas10
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How many GSExxx used for analyse
... Hi, I want to use microarray data to identify DEGs and map its PPI network. To do this, I will use multiple datasets reported by different studies in GEO database. How many min and max data sets (GSExxx) should I use for analyzing? Is there a criteria? I see that is used max 4 GSExxx in several pa ...
geo microarray written 12 weeks ago by cagdas10
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Comment: C: Different results between papers and GEO2R
... Also following paper had found a downregulation. What can be the problem Kevin? https://www.nature.com/articles/s10038-020-0746-6 ...
written 6 months ago by cagdas10
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Comment: C: Different results between papers and GEO2R
... Kevin thank you for your detailed reply. ...
written 6 months ago by cagdas10
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Comment: C: Different results between papers and GEO2R
... Yes, I confirmed it, no problem... ...
written 6 months ago by cagdas10
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Comment: C: Different results between papers and GEO2R
... I did it, and obtained same results. ...
written 6 months ago by cagdas10
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Different results between papers and GEO2R
... Hi, I performed a DE miRNAs analyses via GEO2R for https://www.ncbi.nlm.nih.gov/geo/geo2r/?acc=GSE78775. I obtained an upregulation for miR-148a in tumors compared with normal. When I search miR-148a in Pubmed, unfortunately a lot of paper say it is downregulated (in exp., https://www.ncbi.nlm.nih. ...
microarray geo2r written 6 months ago by cagdas10 • updated 6 months ago by ATpoint44k
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Comment: C: Group definition and logFC calculation in GEO2R
... Thank you Kevin, I will try to write them Best regards ...
written 10 months ago by cagdas10

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