User: avehna

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avehna240
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Posts by avehna

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Answer: A: heatmap without scaling the data
... Hi All, After trying different things, I think it works if instead of plotting the raw data, I apply the *log* function to the data normalized by the control condition... Do you have any other suggestion? Thank you! Avhena On Tue, May 31, 2011 at 1:30 AM, avehna wrote: > Hi All, > > I ...
written 8.4 years ago by avehna240
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heatmap without scaling the data
... Hi All, I am trying to represent my data as a heatmap without scaling it, in such a way that the genes that are upregulated (respect to the control) are "green" and those that are downregulated (respect to the control) are "red". In order to do this, I normalized the data respect to the control, n ...
written 8.4 years ago by avehna240
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Comment: C: Detection calls and LIMMA
... Dear Wolfgang, Thank you for your response, I agree with you. I will read the paper now... Best Regards, Avhena On Mon, Feb 28, 2011 at 4:38 AM, Wolfgang Huber wrote: > Hi Avhena > > it is not required, but properly applied filtering can increase detection > power in your experiment ...
written 8.6 years ago by avehna240
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Detection calls and LIMMA
... Hi All, I have a basic question. Is it required to filter the microarray data based on the detection calls (A/M/P) before analyzing it with LIMMA? What if I have the following scenario (for example): Control Control Control Treatment Treatment Treatment 1367813_ ...
microarray written 8.6 years ago by avehna240 • updated 8.6 years ago by Wolfgang Huber13k
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Comment: C: error under "hclust" for microarray clustering
... Jim, thanks a lot! there were some inf in my data... I will try again after removing then. Avhena On Thu, Jan 27, 2011 at 9:43 AM, James W. MacDonald wrote: > Hi Avhena, > > > On 1/27/2011 12:00 AM, avehna wrote: > >> Hi All, >> >> I'm trying to cluster 21657 gene ...
written 8.7 years ago by avehna240
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Comment: C: error under "hclust" for microarray clustering
... Hi Sean, you were right... there are some inf in my data. Thanks a lot for your help! On Thu, Jan 27, 2011 at 6:04 AM, Sean Davis wrote: > > > On Thu, Jan 27, 2011 at 12:00 AM, avehna wrote: > >> Hi All, >> >> I'm trying to cluster 21657 genes that are differentiall ...
written 8.7 years ago by avehna240
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error under "hclust" for microarray clustering
... Hi All, I'm trying to cluster 21657 genes that are differentially expressed in my microarray data, but it's actually not working for me. After reading the normalized signal and calculating the mean for each treatment I proceed to read the list of genes differentially expressed (previously calculate ...
written 8.7 years ago by avehna240 • updated 8.7 years ago by James W. MacDonald51k
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Answer: A: clustering of microarray time-series data
... Thank you Maciej. I will try it and let you know. Avhena 2010/10/16 Maciej Jończyk > >Message: 13 > >Date: Fri, 15 Oct 2010 14:47:44 -0400 > >From: avehna > >To: "bioconductor@stat.math.ethz.ch" > >Subject: [BioC] clustering of microarray time-series data > &g ...
written 9.0 years ago by avehna240
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clustering of microarray time-series data
... Dear All, I have a time series data from two different samples (treatment A and treatment B) at 3 different time points (0 hr, 6 hr and 24 hr) , the control is time = 0 hr. Both datasets have three replicates. I have already analyzed these data using limma, just to have an idea of regulated genes ...
limma written 9.0 years ago by avehna240
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Comment: C: hclust for 13000 genes
... Hi Steve, I installed the 64-bit version for R and hclust was performed efficiently, however I got the following error during heatmap.2() ----------------------------------------------------------------- Error in image.default(z = matrix(z, ncol = 1), col = col, breaks = tmpbreaks, : breaks mus ...
written 9.6 years ago by avehna240

Latest awards to avehna

Popular Question 8.4 years ago, created a question with more than 1,000 views. For heatmap for high number of genes
Popular Question 8.4 years ago, created a question with more than 1,000 views. For ANOVA vs T-TEST vs eBayes
Popular Question 8.4 years ago, created a question with more than 1,000 views. For error under "hclust" for microarray clustering

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