User: jth

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jth200
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200
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Turkey
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2 years, 4 months ago
Joined:
6 years, 7 months ago
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Posts by jth

<prev • 26 results • page 1 of 3 • next >
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Comment: C: P-value calculation on difference in correlation
... Looks interesting! Thanks a lot! ...
written 3.2 years ago by jth200
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P-value calculation on difference in correlation
... Hi, I have a slightly basic statistics question. I have two large correlation matrices (PCC) (one in wildtype condition, other in treatment condition) of related features. They are about 10000x10000. What i'm interested in is mainly how treatment affects the correlated nature of these features. In ...
statistics written 3.3 years ago by jth200 • updated 3.3 years ago by Jean-Karim Heriche20k
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Comment: C: Downregulated Genes with GFOLD
... Yes, i can't use them as replicate of each other in this case. Each sample has its own control and thats it. ...
written 3.4 years ago by jth200
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Downregulated Genes with GFOLD
... Hi everyone, It'll be a bit long post, so please bear with me. **Background** I have an undesirable set up of unreplicated RNA-seq experiments with matched controls (34 samples and 34 controls). Following a recommendation from Biostars community, I have started using [GFOLD][1] to obtain at least ...
rna-seq written 3.4 years ago by jth200 • updated 3.3 years ago by Biostar ♦♦ 20
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Comment: C: FastQC: Interesting tile quality in paired-end Illumina RNA-seq data
... Thanks for the link! ...
written 3.6 years ago by jth200 • updated 12 months ago by RamRS24k
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FastQC: Interesting tile quality in paired-end Illumina RNA-seq data
... Hi, While performing a quick quality control on raw sequence data of one of the datasets I have downloaded online, I observed me a really interesting per tile sequence quality graph. I have already discarded these files from my analysis, but i'm curious on the possible sources of this phenomenon. O ...
illumina quality control rna-seq fastqc written 3.6 years ago by jth200 • updated 3.6 years ago by Istvan Albert ♦♦ 81k
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Answer: A: how to setup miRDeep2 on osx 10.10 (Yoseimite)
... Hi khblack, Assuming you installed gcc yourself, can you make sure that location of your gcc is in your PATH variable by typing "echo $PATH" in your terminal? If you see any problem you can add the location to your .bash_profile file and re-open a terminal window.  To avoid any complications, you ...
written 3.6 years ago by jth200
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Comment: C: Really Basic Statistics: Expected frequency?
... Thanks a lot! Yes, I look for strand effect as well by doing same calculation for the sense strand and anti-sense strand separately first, then I'm getting a sum of occurrences in both strands and divide by window_size*2 and calculate a obs-to-exp ratio from that as well.  ...
written 3.6 years ago by jth200
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Really Basic Statistics: Expected frequency?
... Hi everyone, I have a question on basic statistics. I feel really bad about asking this but I'm having a brain freeze now. So, i'm going back to basics. Purpose: Calculate expected trinucleotide frequencies specific to 5'UTR regions only, which will be used to check whether some windows (around 20 ...
genome analysis statistics written 3.6 years ago by jth200 • updated 3.6 years ago by Devon Ryan91k
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Filtering transcripts by transcript support level (TSL)
... Hi, I have a question on filtering transcripts from Ensemble by transcription support levels (TSL). Currently, I am collecting Ensembl transcripts for three separate purposes: Calculating nucleotide distributions on exons, introns, and UTRs separately (from canonical transcripts to avoid redunda ...
genome ensembl sequence transcripts written 3.8 years ago by jth200 • updated 2.6 years ago by Vasisht160

Latest awards to jth

Popular Question 2.7 years ago, created a question with more than 1,000 views. For Analyzing Microarray Data In Triplicates With Lumi/Limma (R)
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Comparing Microarray Data From Different Platforms
Popular Question 2.8 years ago, created a question with more than 1,000 views. For Analyzing Microarray Data In Triplicates With Lumi/Limma (R)
Popular Question 2.9 years ago, created a question with more than 1,000 views. For Analyzing Microarray Data In Triplicates With Lumi/Limma (R)
Popular Question 3.6 years ago, created a question with more than 1,000 views. For Analyzing Microarray Data In Triplicates With Lumi/Limma (R)
Popular Question 4.1 years ago, created a question with more than 1,000 views. For Analyzing Microarray Data In Triplicates With Lumi/Limma (R)
Supporter 4.3 years ago, voted at least 25 times.
Popular Question 5.0 years ago, created a question with more than 1,000 views. For Analyzing Microarray Data In Triplicates With Lumi/Limma (R)
Student 5.0 years ago, asked a question with at least 3 up-votes. For Clustering Then Scaling Or Scaling Then Clustering
Student 5.7 years ago, asked a question with at least 3 up-votes. For Multiplicity Testing

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