User: Angel

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Angel210
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United States
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2 years, 4 months ago
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7 years, 2 months ago
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Posts by Angel

<prev • 53 results • page 1 of 6 • next >
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How to assign known subtype based on known gene signature
... Hi All, I have three gene expression signatures and they correspond to three different subtypes. I have a rnaseq data and need to use the three gene signatures to call the three subtypes defined by three gene signatures. What methodologies exist? Naively i can think of just doing a gsea and based ...
subtype rna-seq written 2.4 years ago by Angel210
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Comment: C: comparing RSEM and counts data
... Hi Charles, Please look at my reply to Devon as well. I have pre-normalized dataset for a tumor type which is RSEM on one hand (dataset1) and I do have counts and corresponding RPKM data set for another set of samples (dataset2). The problem at hand is to compare expression of a couple of genes fr ...
written 4.8 years ago by Angel210 • updated 4.8 years ago by Devon Ryan88k
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Comment: C: comparing RSEM and counts data
... Hi Devon,   I am sorry I don't know what you mean. I do not have raw data to work with. I only have RSEM pre-normalized data for a tumor type and only gene counts data (and RPKM) from another data set which refers to normal brain. I am supposed to compare gene expression for few genes from these t ...
written 4.8 years ago by Angel210
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comparing RSEM and counts data
... Hi, I have a RSEM data for a tumor type and I need to compare it gene COUNTS data. Is there a methodology to compare RSEM vs counts? Thanks. ...
rna-seq rsem counts written 4.8 years ago by Angel210 • updated 4.8 years ago by Charles Warden6.4k
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Comment: C: What is the right statistical test that would distinguish between two treatments
... Actually, I have solved my own problem. Thanks for your replies. ...
written 4.9 years ago by Angel210
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Comment: C: What is the right statistical test that would distinguish between two treatments
... The 10 human samples are same, but underwent an expansion phase in mice to create xenografts. For 1st sample e.g., the mutation status of the two mice is exactly the same but one was treated with treatment A and another one with treatment B. ...
written 4.9 years ago by Angel210
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What is the right statistical test that would distinguish between two treatments using a single marker
... I have 10 samples which were treated with two different treatments. For these 10 samples, I have a measure to define that these 10 samples responded differently to the two treatments. Treatment A was active in 9 and inactive in 1 sample. Treatment B was active in 2 and inactive in 8 samples. Also I ...
R statistics association written 4.9 years ago by Angel210 • updated 4.9 years ago by Istvan Albert ♦♦ 79k
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Finding If A Gene Pair Is Paralogous And Accession Ids
... Hello, What do you recommend is a well tested method to find if a gene pair is paralogous. I have about 200 gene pairs to test so I can't really do it manually. A friend recommended using accession IDs and using methods similar to blast. If this is the only method, I have three related questions: ...
written 5.3 years ago by Angel210
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Difference Between Rr Ff And Rf Reads
... Hi: I am wondering which fusion should I prioritize from a couple of candidates. As you know tophat fusion generates a list with the direction of fusion mentioned as well. I am not a biologist and am wondering should I use directionality to prioritize one vs another to investigate further. E.g. ar ...
fusion written 5.4 years ago by Angel210 • updated 5.4 years ago by Devon Ryan88k
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How To Look For Known Fusion In Fastq File
... Hello: I have an internal data for NCI-h660 file with 8m mapped pairs (HiSeq, 50bp paired end data) and I have an external dataset (4m mapped pairs, 50 bp paired end generated on GAII). Questions: 1. I observe TMPRSS2-ERG fusion with external dataset, not with internal data from HiSeq. What could ...
fusion fastq written 5.6 years ago by Angel210 • updated 5.6 years ago by swbarnes25.0k

Latest awards to Angel

Appreciated 4.8 years ago, created a post with more than 5 votes. For How To Generate Alignment Statistics Report?
Great Question 4.8 years ago, created a question with more than 5,000 views. For Obtaining Exon Lengths:
Great Question 4.8 years ago, created a question with more than 5,000 views. For How To Generate Alignment Statistics Report?
Good Question 4.8 years ago, asked a question that was upvoted at least 5 times. For How To Generate Alignment Statistics Report?
Popular Question 4.8 years ago, created a question with more than 1,000 views. For Finding Somatic Mutations From Whole Exome
Popular Question 4.8 years ago, created a question with more than 1,000 views. For Obtaining Exon Lengths:
Popular Question 4.8 years ago, created a question with more than 1,000 views. For Obtaining Aa Position From Snpeff Output:
Popular Question 4.8 years ago, created a question with more than 1,000 views. For How To Set Filter For Frequency Of Reads And Hapmap Exome Sample Results:
Popular Question 4.8 years ago, created a question with more than 1,000 views. For How To Randomly Select 20M Reads From A 200M Fastq File
Popular Question 4.8 years ago, created a question with more than 1,000 views. For Bcftools Mpileup Removes Marked Duplicates?
Popular Question 4.8 years ago, created a question with more than 1,000 views. For Output From Picard And Samtools Flagstat Not Very Useful From My Sambam Files:
Popular Question 4.8 years ago, created a question with more than 1,000 views. For How To Generate Alignment Statistics Report?
Popular Question 4.8 years ago, created a question with more than 1,000 views. For Difference Between Rr Ff And Rf Reads
Popular Question 4.8 years ago, created a question with more than 1,000 views. For Option "Calmd" For Whole-Exome Is Very Confusing:
Popular Question 4.8 years ago, created a question with more than 1,000 views. For Marking Duplicates And Comparing 2 Samples?
Student 7.1 years ago, asked a question with at least 3 up-votes. For 2-3 Example Datasets (References) With Known Variants?
Popular Question 7.1 years ago, created a question with more than 1,000 views. For Output From Picard And Samtools Flagstat Not Very Useful From My Sambam Files:
Popular Question 7.1 years ago, created a question with more than 1,000 views. For How To Generate Alignment Statistics Report?
Student 7.1 years ago, asked a question with at least 3 up-votes. For How To Generate Alignment Statistics Report?
Popular Question 7.2 years ago, created a question with more than 1,000 views. For Obtaining Exon Lengths:
Student 7.2 years ago, asked a question with at least 3 up-votes. For Obtaining Exon Lengths:

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