User: bharata1803

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bharata180320
Reputation:
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New User
Location:
Japan
Last seen:
3 days, 10 hours ago
Joined:
3 years, 6 months ago
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b**********@gmail.com

Posts by bharata1803

<prev • 51 results • page 1 of 6 • next >
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Comment: C: DESeq2 with several biological replicates
... hello, it seems it is not biological replicates but technical replicates. the biological sample is the same. it just run/sequenced 5 times. Can you give some suggestion? If not, I will just take 1 sample from every patient to make things simpler. If it is from the same sample and just sequence 5 tim ...
written 6 days ago by bharata180320
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Comment: C: DESeq2 with several biological replicates
... Actually it is a public data. So, I am not so sure myself. This is the link: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=SRP069212 From the paper, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5316832/ they only mentioned like this: Total RNA from 60 samples from 20 Chinese HCC patients was sequ ...
written 9 days ago by bharata180320
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Comment: C: DESeq2 with several biological replicates
... The number of patients is 20. Each patients has 5 normal rna-seq reads and 5 tumor rna-seq reads (matched). ...
written 10 days ago by bharata180320
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DESeq2 with several biological replicates
... Hello, Is there any guide or tutorial to process RNA-seq sample with biological replicates? I have 2 conditions, normal and tumor. The total number of sample is 20 with each normaland tumor has 5 biological replicates. Thanks. ...
rnaseq deseq2 differential gene expression written 10 days ago by bharata180320
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WGCNA package : identification of hub genes
... I have a research problem that I want to solve. Basically, I want to find important genes per module that is generated from WGCNA algorithm. I define important genes as hub genes. Hub genes is defined as genes that have most connectivity. I read from some paper that basically the calculation is to ...
wgcna written 10 months ago by bharata180320
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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 12 months ago by bharata180320
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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 12 months ago by bharata180320
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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 12 months ago by bharata180320
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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 12 months ago by bharata180320
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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 12 months ago by bharata180320

Latest awards to bharata1803

Popular Question 20 months ago, created a question with more than 1,000 views. For Limma log transform RNA-seq and microarray
Popular Question 20 months ago, created a question with more than 1,000 views. For DESeq2 with multiple conditions
Popular Question 20 months ago, created a question with more than 1,000 views. For DESeq2 Error NA values
Popular Question 20 months 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 20 months ago, created a question with more than 1,000 views. For DESeq2 Error NA values
Popular Question 2.5 years ago, created a question with more than 1,000 views. For DESeq2 rlog function takes too long

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