User: morteza.hadizade

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Posts by morteza.hadizade

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Comment: C: extracting the genes associated with the groups or samples in pheatmap.
... Hi Kevin, Thank you so much, your answer was reasonable and accurate. According to your guidance, If I want to extract a gene list, I should use the cutree command, in this command, can I use the sample number instead of the cluster number? I have 73 sample.     ...
written 12 days ago by morteza.hadizade10
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Comment: C: extracting the genes associated with the groups or samples in pheatmap.
... Dear Malcolm, Thank you I really appreciate your help. ...
written 12 days ago by morteza.hadizade10
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Comment: C: extracting the genes associated with the groups or samples in pheatmap.
... Hi, Thank you for pointing this out. these genes are reported in an article, I get those from a supplementary file, I want to compare the genes of each group with my results. The gene list published in the supplementary file was a matrix, I clustered it by creating a pheatmap, but I could not extra ...
written 17 days ago by morteza.hadizade10
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extracting the genes associated with the groups or samples in pheatmap.
... Hi everyone I have an expression matrix, the rows contain 995 significant genes and columns contain 73 sample (995*73), samples are divided into 4 groups, after generation of heat map (pheatmap) from this matrix, how can I extract the genes associated with the groups or any sample? I would be very ...
microarray R written 18 days ago by morteza.hadizade10 • updated 17 days ago by Malcolm Cook1.5k
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Comment: C: remove NAs values from gset
... Thank you so much for your valuable guidance, your answer was reasonable and accurate. ...
written 9 weeks ago by morteza.hadizade10
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Comment: C: Compare in cont.matrix part
... Thank you for your help ...
written 9 weeks ago by morteza.hadizade10
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Comment: C: Compare in cont.matrix part
... Thank you for your answer, but LogFC is important in our results final (up and down-regulated genes), if I remove the single quotes, LogFC is removed from the analysis result. So I have to compare two groups in cont.matrix. ...
written 9 weeks ago by morteza.hadizade10
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Compare in cont.matrix part
... Hi everyone, In the cont.matrix, can I compare each individual group separately (Not altogether)? Thanks you very much for your attention.   cont.matrix<- makeContrasts (TGFbeta-Control, levels=design) or cont.matrix<- makeContrasts (SSc – Control, levels=design) instead cont.matrix< ...
microarray R written 10 weeks ago by morteza.hadizade10 • updated 9 weeks ago by Gordon Smyth35k
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remove NAs values from gset
... Hi everyone Sometimes in microarray analysis, “ex” matrix is contained any NA values, I remove NAs with “na.omit” command, after removing NAs from “ex” matrix, do I need to remove NAs from “gset”??? I would be very pleased if you could guide me.   gset <- getGEO(dataset, GSEMatrix =TRUE, Anno ...
microarray R written 10 weeks ago by morteza.hadizade10 • updated 9 weeks ago by James W. MacDonald48k

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