User: Jamal

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Jamal0
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Posts by Jamal

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Meta_analysis of microarray data
... In the meta-analysis of three microarray datasets, we have different cell lines of the same cancer type with distinct platforms. In your idea is it logical to compare deferentially expressed genes in these derivatives of a cancer? ...
microarray platform meta analysis microarray data written 7 months ago by Jamal0 • updated 7 months ago by James W. MacDonald51k
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Meta_analysis of different platforms of microarray data
... Hi Dears… In a meta-analysis study, I am trying to find DEGs from different individual studies with platforms like 3D-Gene Human Oligo chip 25k V2.1, Affymetrix Human Genome U133 Plus 2.0 Array, Affymetrix Human Genome U133 Plus 2.0 Array, Agilent-014850 Whole Human Genome Microarray 4x44K G4112F a ...
microarray cancer R software meta analysis written 9 months ago by Jamal0 • updated 9 months ago by James W. MacDonald51k
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Comment: C: making contrast in limma for Affymetrix data
... Dear Aaron, I already read the user guide. Unfortunately, I did not fully understand this section and I doubt it in the results. I will be very grateful if you resolve my doubt. ...
written 19 months ago by Jamal0 • updated 19 months ago by Gordon Smyth38k
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Comment: A: making contrast in limma for Affymetrix data
... all samples were processed in PBMEC (in vitro bovine mammary epithelial cells) and at the same time. I want to get DEs which up or down-regulated in Q genotype compare with q genotype! I think so but I don't sure, do my contrast code following is correct? cont.matrix <- makeContrasts(   ...
written 19 months ago by Jamal0 • updated 19 months ago by Gordon Smyth38k
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Comment: C: making contrast in limma for Affymetrix data
... Dear Aaron , Are you sure that it is possible to compare betweens genotypes directly? Diff_1C = Q.1.C - q.1.c, Diff_1E = Q.1.E - q.1.e, And one more question is how to learn to do these comparisons, generally?   Thank you again for your patience and guidance !! ...
written 19 months ago by Jamal0
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Comment: C: making contrast in limma for Affymetrix data
... I have a trouble with making a contrast matrix. First, compare the treatment of the genotypes with their controls, then I would like to compare the two genotypes (the problem is related to this section,  there is no error, but none of the genes are not significant).  Diff_1h = (Q.1.E - Q.1.C) - (q ...
written 19 months ago by Jamal0
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(Closed) making contrast in limma for Affymetrix data
... hi guys,  I want to create a contrasts matrix to compare the Affymetrix array (two types of genotypes, two treatment groups (infected) and controls for each genotype and three times for each genotype), for comparison, I wrote the code below Please guide. Where is the problem? TF <- paste(P1$Ge ...
microarray limma affymetrix design and contrast matrix contrast matrix written 20 months ago by Jamal0 • updated 19 months ago by Gordon Smyth38k
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Comment: C: Identify up and down regulated genes in affymetrix data
... Thank you very much for your explanation. Would you please explain how  to choose such thresholds for LogFC. (logFC>=0.58 (i.e. 1.5 fold up) or logFC<=-0.58 (i.e. 1.5 fold down) ) ...
written 2.2 years ago by Jamal0
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Comment: C: Identify up and down regulated genes in affymetrix data
...   Thank you for your consideration, but there is something misunderstanding for me, how can I detect UP and DOWN genes after detection the differentially expression genes? (In some sites I have seen they considered the fold change higher than 0 as UP and less than 0 as DOWN. It should be noted that ...
written 2.2 years ago by Jamal0
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Comment: C: Identify up and down regulated genes in affymetrix data
... Thank you for your consideration, but there is something misunderstanding for me, how can I detect UP and DOWN genes after detection the differentially expression genes? (In some sites I have seen they considered the fold change higher than 0 as UP and less than 0 as DOWN. It should be noted that li ...
written 2.2 years ago by Jamal0

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Popular Question 9 months ago, created a question with more than 1,000 views. For Identify up and down regulated genes in affymetrix data

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