User: grayapply2009

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grayapply2009170
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Posts by grayapply2009

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Comment: C: Why are transcripts of a same gene expressed differently in same samples?
... That sounds reasonable, goodez. ...
written 17 months ago by grayapply2009170
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Comment: C: Why are transcripts of a same gene expressed differently in same samples?
... But the ratio should not change, right? RNAseq: Variant 1 / Variant 2 = 25 qPCR: Variant 1 / Variant 2 = 10 How do you explain this? ...
written 17 months ago by grayapply2009170
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Comment: A: Why are transcripts of a same gene expressed differently in same samples?
... Another question, we did qPCR to validate the RNAseq results. We found less difference between our "major isoform" and all other isoforms than what we found in RNAseq. Is this just a technical difference or does this have something to do with biology? ...
written 17 months ago by grayapply2009170
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Why are transcripts of a same gene expressed differently in same samples?
... We recently did RNA-seq for our samples and quantified the expression levels of the 7 transcripts of one gene. We found one of these transcripts are expressed significantly higher (30x) than other transcripts across all of our samples. Any explanation for this constantly high expression for a singl ...
transcript expression rna-seq written 17 months ago by grayapply2009170 • updated 12 months ago by kristoffer.vittingseerup2.6k
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Comment: C: Sample size too small for ARACNE
... Thank you very much for replying my post. There is a computer algorithm (ARACNE) that can reconstruct gene regulatory networks from gene expression profiles. However, it requires a minimum of 100 gene expression profiles, for example, 100 microarray datasets. I only have 20 of these datasets so I gu ...
written 2.7 years ago by grayapply2009170
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Comment: C: How to annotate GEO microarray datasets with GEOquery?
... Thank you, gaoce. That works perfectly. Where can I get the tutorial for this? The GEOquery document doesn't seem to have what you guys showed me above. ...
written 3.2 years ago by grayapply2009170
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Comment: C: How to annotate GEO microarray datasets with GEOquery?
... Thank you Sean. Now how can I export the Series Matrix file with the probes replaced by gene symbols? ...
written 3.2 years ago by grayapply2009170
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How to annotate GEO microarray datasets with GEOquery?
... Hi, I read the GSE file into R as follows. gse <- getGEO("GSE4928", GSEMatrix=TRUE) Now I want to convert all probe IDs to gene symbols and write the entire annotated dataset back to my computer. What should I do? By the way, which dataset is stored in gse? SOFT formatted family file, MINiML ...
geo annotation microarray written 3.2 years ago by grayapply2009170 • updated 3.2 years ago by Sean Davis25k
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Collapse and average the microarray data
... I have a microarray data set. The format is like this: a 12 13 14 b 15 16 17 a 21 22 23 b 24 25 26 Now I want to collapse and average all rows and columns based on the gene name (the 1st line). The desired results: a 16.5 17.5 18.5 b 19.5 20.5 21.5 T ...
average microarray awk written 3.2 years ago by grayapply2009170
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Comment: C: Pooling microarray data
... Looks like a lot of trouble. I'll just merge the arrays done on the same platform I can find. Thank you very much, Jean. ...
written 3.2 years ago by grayapply2009170

Latest awards to grayapply2009

Great Question 17 months ago, created a question with more than 5,000 views. For How to generate a fasta file from a python dictionary or lists?
Popular Question 2.7 years ago, created a question with more than 1,000 views. For interproscan5 doesn't work for nucelotide sequences but works for protein sequences??
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Any tutorials for Trinotate?
Popular Question 2.7 years ago, created a question with more than 1,000 views. For How to retrieve gene symbols with refseq protein accesion number or gi number?
Popular Question 2.7 years ago, created a question with more than 1,000 views. For How to generate a fasta file from a python dictionary or lists?
Popular Question 2.7 years ago, created a question with more than 1,000 views. For How to find start and stop codon for sequences in a fasta file?
Student 2.7 years ago, asked a question with at least 3 up-votes. For How to annotate GEO microarray datasets with GEOquery?
Popular Question 3.1 years ago, created a question with more than 1,000 views. For interproscan5 doesn't work for nucelotide sequences but works for protein sequences??
Popular Question 3.1 years ago, created a question with more than 1,000 views. For What does interproscan add to gene annotation?
Popular Question 3.1 years ago, created a question with more than 1,000 views. For Any tutorials for Trinotate?
Popular Question 3.1 years ago, created a question with more than 1,000 views. For How to generate a fasta file from a python dictionary or lists?
Popular Question 3.1 years ago, created a question with more than 1,000 views. For How to find start and stop codon for sequences in a fasta file?
Popular Question 3.1 years ago, created a question with more than 1,000 views. For Why the local blast and online blast produce different results?
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Popular Question 3.4 years ago, created a question with more than 1,000 views. For How to find start and stop codon for sequences in a fasta file?
Popular Question 3.4 years ago, created a question with more than 1,000 views. For How to generate a fasta file from a python dictionary or lists?
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