User: Jamal

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Jamal0
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Posts by Jamal

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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 7 months ago by Jamal0 • updated 7 months ago by Gordon Smyth35k
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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 7 months ago by Jamal0 • updated 7 months ago by Gordon Smyth35k
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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 7 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 7 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 7 months ago by Jamal0 • updated 7 months ago by Gordon Smyth35k
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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 14 months 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 15 months 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 15 months ago by Jamal0
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Identify up and down regulated genes in affymetrix data
... Dear All, How can I recognize (detect) ups and downs genes where  "Limma" genes have been Significant?  What threshold do you recommend to use in this matter?  I was wondering If you could explain me why this threshold have been chosen. Thank you so much ...
microarray affy limma written 15 months ago by Jamal0 • updated 14 months ago by tg36940

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