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User: anandprem1792

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Posts by anandprem1792

<prev • 6 results • page 1 of 1 • next >
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Do we need to filter out control probes and low expressed probes (as given in LIMMA user guide 2016 page number 111) for all Agilent microarray platform
... I am analyzing a GEO dataset of platform (GPL17077) Agilent-039494 SurePrint G3 Human GE v2 8x60K Microarray. I followed the steps given in LIMMA user guide 2016 (page number 110-112). The protocol given there is for Agilent 4x44K Arrays. So my question is whether i have to filter out control probes ...
agilent microarray limma written 21 months ago by anandprem1792 • 20 • updated 19 months ago by Biostar ♦♦ 20
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Comment: C: Is fold change of value 1.5 (log2FC = 0.58) a significant value ?
... Thank you for the suggestion. As you said I will filter by "adjusted p-value" first. ...
written 21 months ago by anandprem1792 • 20
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Comment: C: Is fold change of value 1.5 (log2FC = 0.58) a significant value ?
... Thank you for the help. ...
written 21 months ago by anandprem1792 • 20
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Is fold change of value 1.5 (log2FC = 0.58) a significant value ?
... In Biostars forum for differential gene expression analysis by LIMMA I found that most people suggest to set a threshold value of Log2FC > or = 2 to filter DEGs. When I analyzed the GEO dataset "GSE90594" - Agilent-039494 SurePrint G3 Human GE v2 8x60K Microarray 039381 platform for DEGs by LIMM ...
agilent limma microarray analysis written 21 months ago by anandprem1792 • 20 • updated 21 months ago by WouterDeCoster ♦ 45k
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How to download PPI network file from Reactome database for a list of genes and view them in cytoscape ?
... Can anyone tell me how to download the PPI network file from REACTOME database. I want to view that file in cytoscape. In which format I should download the file in reactome ? ...
reactome cytoscape written 3.3 years ago by anandprem1792 • 20 • updated 3.3 years ago by Jean-Karim Heriche ♦ 24k
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Differential Gene expression analysis and Gene ontology analysis
... Can anyone suggest me a good tutorial for gene expression analysis from microarray data. Please provide links for the tutorials thanks. ...
gcrma gene expression analysis affy limma written 3.5 years ago by anandprem1792 • 20 • updated 3.5 years ago by h.mon ♦ 32k

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