User: Liat Shavit Grievink

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Posts by Liat Shavit Grievink

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Comment: C: Row labels in a heatmap
... Yay!! Thank you so much! On 16.07.2012, at 16:46, James W. MacDonald wrote: > OK, so just set it to be so. > > nam <- rep("", nrow(yourmatrix)) > nam[seq(1,nrow(yourmatrix), 100)] <- seq(1, nrow(yourmatrix), 100) > row.names(yourmatrix) <- nam > > Best, > > Jim & ...
written 5.4 years ago by Liat Shavit Grievink60
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Comment: C: Row labels in a heatmap
... Hi James, Thank you! The thing is that I rather not have numbers 1 to 500, but for example: 1, 100, 200, 300,400, 500. or something like this (so show a label only every 100 genes). Thanks again, Liat. On 16.07.2012, at 16:24, James W. MacDonald wrote: > row.names(yourmatrix) <- seq(1, nrow(y ...
written 5.4 years ago by Liat Shavit Grievink60
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Row labels in a heatmap
... Hi all, I'm trying to draw a heatmap for some microarray data. Since I have many genes, the gene names (row labels) are not readable. I would like to replace these gene names by seq(0,500,by=100). Any ideas on how to do that? I tried both heatmap and heatmap.2, but couldn't find a good way to do th ...
microarray written 5.4 years ago by Liat Shavit Grievink60 • updated 5.4 years ago by James W. MacDonald45k
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Comment: C: Affy mas5 scaling
... Thank you. Yhe I would like to use RMA but for now I'm trying to repeat someone former results. The problem is that I am getting twice as many genes. And the expression values are extremely different. Why is the scaling so random and different from the one done by affymetrix MAS5? Cheers, Liat. Dat ...
written 5.4 years ago by Liat Shavit Grievink60
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Affy mas5 scaling
... Hi all, I have some raw data as well as Affymetrix MAS5 normalized data for oligonucleotide arrays. For the raw data I use the mas5 function of the affy package. >From then on I run the same code on both (removing AFFY controls, applying log, selecting genes over a certain fold change etc.). I e ...
normalization affy written 5.4 years ago by Liat Shavit Grievink60 • updated 5.4 years ago by yao chen200
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Answer: A: help needed - 7 array time course gene expression no replicates - fold change ca
... Dear James, Just wanted to thank you for your detailed reply. It was very helpful! It gives me a lot to think about. I will use fold change for now to get an idea of what is there, and discuss possible assumptions with the person who was involved in the experiment design (I wasn't...). Thanks again! ...
written 5.4 years ago by Liat Shavit Grievink60

Latest awards to Liat Shavit Grievink

Great Question 5.4 years ago, created a question with more than 5,000 views. For Row labels in a heatmap
Popular Question 5.4 years ago, created a question with more than 1,000 views. For Row labels in a heatmap

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