User: vish

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vish70
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Posts by vish

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Comment: C: Differential expression analysis for log2(x+1) transformed RSEM normalized count
... This is where I got the data (https://xenabrowser.net/datapages/?dataset=TCGA.LIHC.sampleMap/HiSeqV2&host=https://tcga.xenahubs.net) When I click on the rawdata for download it gives page isn't working. ...
written 10 days ago by vish70
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Comment: C: Differential expression analysis for log2(x+1) transformed RSEM normalized count
... Thank you. I see that they are using library(curatedCRCData) to get the data. CRC is colorectal. I want the data for liver. I tried giving curatedliverData it says not available. ...
written 10 days ago by vish70
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Differential expression analysis for log2(x+1) transformed RSEM normalized count (TCGA)
... Hello everyone, I have retrieved the rnaseq data from TCGA. The data is Level_3 Data (file names: *.rsem.genes.normalized_results) downloaded from TCGA, shows the gene-level transcription estimates, as in log2(x+1) transformed RSEM normalized count. Data looks like this: sample TCGA ...
differential analysis R tcga rna-seq written 11 days ago by vish70 • updated 11 days ago by trollchenok0
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Comment: C: How Do I Draw A Heatmap In R With Both A Color Key And Multiple Color Side Bars?
... Hi, In the above heatmap how to get all "Basal" subtype as one cluster? I mean all samples showing red should be clustered. In the same way other subtypes also. I see that sample() function which is used for creating fake colors randomly reorders the elements. But I don't want to do that. So how can ...
written 14 days ago by vish70
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Comment: C: How Do I Draw A Heatmap In R With Both A Color Key And Multiple Color Side Bars?
... Hi, In the above heatmap given by Obi griffith how to get all "Basal" subtype as one cluster? I mean all samples showing red should be clustered. In the same way other subtypes also. I see that sample() function which is used for creating fake colors randomly reorders the elements. But I don't want ...
written 14 days ago by vish70
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Comment: C: Visualization of Amplification and deletion data with genes : CNV
... Yes, it worked. But it is with 20k genes so its huge. not able to showup here. ...
written 17 days ago by vish70
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Comment: C: Visualization of Amplification and deletion data with genes : CNV
... So, now I generated a heatmap showing amplifications and deletions of genes. Copy <- read.delim("cnv_data",as.is = T) Copy2 <- data.frame(Copy[,-1], row.names=Copy[,1]) heatmap.3(Copy2) ...
written 17 days ago by vish70
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Comment: C: Visualization of Amplification and deletion data with genes : CNV
... Sorry, I was confused. Its not correlation. I want to see the copy number regulation of genes which show copy number loss. I have the CNV data with me. ...
written 17 days ago by vish70
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Comment: C: Visualization of Amplification and deletion data with genes : CNV
... Yes I understood what I said. I just thought of showing an example plot. That is why I posted the link. ...
written 17 days ago by vish70
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Comment: C: Visualization of Amplification and deletion data with genes : CNV
... What I want is something like this (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3146966/figure/F1/) ...
written 17 days ago by vish70

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