User: bharata1803

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bharata180340
Reputation:
40
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New User
Location:
Japan
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3 weeks, 1 day ago
Joined:
3 years, 11 months ago
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b**********@gmail.com

Posts by bharata1803

<prev • 56 results • page 2 of 6 • next >
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Comment: C: DESeq2 result really different when only use some sample vs all sample
... The reason I subset my sample is the DESeq2 log fold change is really weird. There are not many genes that are differentially expressed and only around ~600 genes with p-value adjusted less than 0.05 (~500 genes have logfoldchange >0.65 or <-0.65, |0.65| is my cut for up/down regulated). So, I ...
written 18 months ago by bharata180340
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Comment: C: DESeq2 result really different when only use some sample vs all sample
... Additional info, I have processed both all sample and subset sample read count matrix using Limma/Voom and the result is more weird. If I compare log fold change result between DESeq2 and Limma/Voom for subset sample, the logfoldchange data is really similar. If I calculate Pearson correlation of lo ...
written 18 months ago by bharata180340
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Comment: C: DESeq2 result really different when only use some sample vs all sample
... I don't understand which object that you mean. In that code, it is really simple I think. Line 5 and 6 is reading from inputted file and line 7 actually setting the category. In the TCGA data, there are 3 types of sample type, Solid Tumor Tissue, Solid Tissue Normal, and Recurrent Tumor. In that li ...
written 18 months ago by bharata180340
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Comment: C: DESeq2 result really different when only use some sample vs all sample
... Hello, I've updated the post with the code that I used and my session info ...
written 18 months ago by bharata180340
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DESeq2 result really different when only use some sample vs all sample
... Hello, So, I have read count matrix from TCGA LIHC and its metadata. The project consist of around 400 samples (around 50 normal). I have run DESeq2 to calculate logfoldchange and log expression. I have the result. Then, I decided to do some clustering to get smaller size of the samples. From thi ...
rnaseq deseq2 written 18 months ago by bharata180340
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Comment: C: DEseq2: any problem with unbalanced number of sample in normal/tumor study?
... I am not in a hurry and my computer is quite good. For almost 600 samples, it took around 1 hour so I think no problem. As for getting the log transform of read count for expression level from the sample, maybe it will take really long time. In this post : https://support.bioconductor.org/p/77122/ I ...
written 18 months ago by bharata180340
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DEseq2: any problem with unbalanced number of sample in normal/tumor study?
... Hello, I have downloaded TCGA datasets (htseq count file) for several cancer disease. I realized that each dataset has large number of tumor sample but not the normal sample. For example only 60 samples normal and up to ~500 or more tumor samples. Will this unbalance sample cause any problem if I u ...
rnaseq deseq2 tcga written 18 months ago by bharata180340 • updated 18 months ago by Michael Love23k
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DESeq2 for read count input from 2 different NGS platforms
... I want to do some differential expression analysis for cancer data. I have found the cancer data from TCGA which is hosted by GDC. Unfortunately, the data doesn't include normal sample. All data comes from cancer sample. I tried to find another data from the cancer I want to analyze which include no ...
rnaseq deseq2 written 2.1 years ago by bharata180340 • updated 2.1 years ago by Ryan C. Thompson7.3k
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Answer: A: Deseq2 results interpretation
... Hello, I am not an expert but I have done multiple factor before although simpler than yours which is comparison for 3 phenotypes.   Answering your question, I think fast vs slow is all data in fast category vs all data in slow category. There is no time separation. RT vs 15, RT vs 90, 15 vs  90 ...
written 2.9 years ago by bharata180340
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Comment: C: Generate sample data based on DESeq2 result
... Thank you so much. I will try your suggestion. ...
written 3.1 years ago by bharata180340

Latest awards to bharata1803

Popular Question 2.1 years ago, created a question with more than 1,000 views. For Limma log transform RNA-seq and microarray
Popular Question 2.1 years ago, created a question with more than 1,000 views. For DESeq2 with multiple conditions
Popular Question 2.1 years ago, created a question with more than 1,000 views. For DESeq2 Error NA values
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Calculate DESeq2 fold change of 1 gene to 1 of the sample
Popular Question 2.1 years ago, created a question with more than 1,000 views. For DESeq2 Error NA values
Popular Question 2.9 years ago, created a question with more than 1,000 views. For DESeq2 rlog function takes too long

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