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Search: Posts Made By: idyll_ty
Forum: Bioinformatics 03-03-2012, 07:36 PM
Replies: 5
Views: 3,412
Posted By idyll_ty
Have you solved this problem? I also have this...

Have you solved this problem? I also have this problem, and I'm very interested in the result.
Forum: Bioinformatics 02-18-2012, 10:58 PM
Replies: 0
Views: 1,554
Posted By idyll_ty
tophat paired end read alignment

Hi, I am doing paired end alignment using tophat. Since I'm new to this program, I'm a little confusing about the format of the alignment output: accepted_hits.bam. How can I determine which read end...
Forum: RNA Sequencing 01-04-2012, 10:55 PM
Replies: 1
Views: 1,472
Posted By idyll_ty
Why edgeR ouput some p values larger than 1

I was using edgeR to do differential expression on a RNA-seq dataset, but when I check the p.value distribution of the output, I found ~700 genes got a p value larger than 1... Just wondering if...
Forum: RNA Sequencing 11-01-2011, 09:49 PM
Replies: 8
Views: 6,460
Posted By idyll_ty
Yes, the genes names are consistent. I find...

Yes, the genes names are consistent.

I find the problem. Because in my input read count data, for some genes, there are no reads mapped at all, and those genes cause NA values in the results.
Forum: RNA Sequencing 11-01-2011, 08:56 PM
Replies: 8
Views: 6,460
Posted By idyll_ty
DESeq: "NA" generated in the resulted differentially expressed genes

I am using DESeq to analyze my RNA-seq data. However, I found in my generated differentially expressed genes there were a a bunch of "NA". Please see the attached table for details. The number of...
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