User: Ashwini Patil

gravatar for Ashwini Patil
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New User
Location:
San Francisco Bay Area
Last seen:
6 months ago
Joined:
4 years, 8 months ago
Email:
p****************@gmail.com

Posts by Ashwini Patil

<prev • 12 results • page 1 of 2 • next >
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Answer: A: How to view TCGA data in idat format file.
... You can use minfi R package (https://bioconductor.org/packages/3.3/bioc/manuals/minfi/man/minfi.pdf) to read and normalize idat files. targets <- read.450k.sheet(baseDir) sub(baseDir, "", targets$Basename) RGset <- read.450k.exp(base = baseDir, targets = targets) ...
written 17 months ago by Ashwini Patil70
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Comment: C: resem values from TCGA RNAseqV2 data
... Thanks guys! That helped. My original approach was to remove all values that were < 1. But log2(rsemvalue+1) also sounds reasonable. For plotting the heatmap https://www.biostars.org/p/73644/ this post helped a lot. ...
written 2.8 years ago by Ashwini Patil70
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Comment: C: resem values from TCGA RNAseqV2 data
... I want to know if the RSEM values obtained from TCGA (.rsem.genes.normalized_results) can be used directly for heatmap after log transformation. Should the RSEM values be covered to transcripts per million (TPM)? Should it be also normalized across samples (if so how)? It is difficult to get this in ...
written 2.8 years ago by Ashwini Patil70
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resem values from TCGA RNAseqV2 data
... Hi all, I am working with TCGA RNAseqV2 data and the data consist of rsem values. rsem values have huge variations so I took log2(rsem) and plotted a heatmap. I am interested in seeing expression level. My question is: are rsem values comparable to all sample particularly expression? Thanks, Ash ...
tcga rna-seq written 2.8 years ago by Ashwini Patil70 • updated 2.8 years ago by Biostar ♦♦ 20
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Comment: C: How To Interpret The Output Generated By The Calc-Bmr Music By Washu
... hi, I am sorry to come back to this so late. I checked there is no problem with other files. The thing is that I have only 1 mutation per gene mentioned in the maf file. If we see the above example, there are 7 mutations listed in maf file. In the results from bmr it lists 7 mutations for each gene ...
written 4.6 years ago by Ashwini Patil70
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Comment: C: How To Interpret The Output Generated By The Calc-Bmr Music By Washu
... Thank you so much for the quick reply. I am extermely sorry to be so clumsy. I have revised my question. ...
written 4.7 years ago by Ashwini Patil70
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How To Interpret The Output Generated By The Calc-Bmr Music By Washu
... hi, I have 7 genes from 1 sample I am trying to analyze. In the result, the total no. of mutations for every gene is shown as the total no. of genes I have provide in the maf file. #Gene Indels SNVs Tot Muts MARCH12 0 7 7 JUNE12 0 7 7 .... Here, for every gene it shows 7 ...
genome music written 4.7 years ago by Ashwini Patil70 • updated 4.7 years ago by Cyriac Kandoth4.6k
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Comment: C: Problems Running Bmr Calc-Covg On Music By Washu
... my roi file had problems. I am able to run smg now. Thank You! ...
written 4.7 years ago by Ashwini Patil70
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Comment: C: Problems Running Bmr Calc-Covg On Music By Washu
... Thanks a lot. Now I am able ti run calc-covg and calc-bmr but am facing problems running smg. I get the following error. genome music smg --gene-mr-file /home/dell/Downloads/output/gene_mrs --output-file /home/dell/Downloads/output/smgs Error in data.frame(..., check.names = FALSE) ...
written 4.7 years ago by Ashwini Patil70
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Comment: C: Problems Running Bmr Calc-Covg On Music By Washu
... I tried this got the following errors. ...
written 4.7 years ago by Ashwini Patil70

Latest awards to Ashwini Patil

Popular Question 2.8 years ago, created a question with more than 1,000 views. For resem values from TCGA RNAseqV2 data
Popular Question 2.8 years ago, created a question with more than 1,000 views. For How To Interpret The Output Generated By The Calc-Bmr Music By Washu
Popular Question 2.8 years ago, created a question with more than 1,000 views. For Problems Running Bmr Calc-Covg On Music By Washu

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