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Forum: RNA Sequencing 11-26-2015, 02:55 AM
Replies: 9
Views: 9,891
Posted By DPCook
Yeah, log transformation may be a good thing to...

Yeah, log transformation may be a good thing to do prior to Z-score calculation

Because you have dendrogram="column", I'm guessing you have samples in the columns, right? I notice two things about...
Forum: RNA Sequencing 11-25-2015, 03:35 PM
Replies: 9
Views: 9,891
Posted By DPCook
No problem! Transform one of the values that...

No problem!

Transform one of the values that takes into account total number of reads (ie. FPKM or TPM) so that differences in sequencing depth between samples don't affect things.

The...
Forum: RNA Sequencing 11-25-2015, 04:35 AM
Replies: 9
Views: 9,891
Posted By DPCook
Hi Silvia, What scripts are you using at the...

Hi Silvia,

What scripts are you using at the moment? That may help narrow in on the problem, if one exists. If you're not, scaling the expression values (eg. Z-score transformation) for each gene...
Forum: Bioinformatics 08-07-2015, 06:21 AM
Replies: 5
Views: 993
Posted By DPCook
I kind of fell into this computation stuff about...

I kind of fell into this computation stuff about a year ago with no formal background in computer science, so I understand where you're coming from.

First, as emphasize above, ditch excel for...
Forum: RNA Sequencing 03-13-2015, 04:49 AM
Replies: 3
Views: 3,452
Posted By DPCook
Thanks for the reply Michael. I adjusted the lfc...

Thanks for the reply Michael. I adjusted the lfc threshold and it certainly made the list a bit more manageable (LFC > 1.5, FDR=0.05 yielded about 800 DEGs in both directions). I guess I just wasn't...
Forum: RNA Sequencing 03-12-2015, 08:01 AM
Replies: 3
Views: 3,452
Posted By DPCook
Questionable diagnostic plots from Cummerbund/DESeq2

Hi everyone,

I'm analyzing some RNA-seq data for a colleague and some of the results/diagnostic plots have raised some caution flags in my mind. I'll include the code I used to avoid going back...
Forum: Bioinformatics 12-10-2014, 02:04 PM
Replies: 3
Views: 953
Posted By DPCook
I second this. Circos plot with histogram tracks...

I second this. Circos plot with histogram tracks for each tissue could look really good. The only problem I can see would be resolution. If you want to show differences within small ranges (eg....
Forum: Bioinformatics 12-10-2014, 09:49 AM
Replies: 0
Views: 2,057
Posted By DPCook
Truncated File: Trouble with SRA > Fastq > Sam

Hi everyone,

I know there have been several posts regarding truncated SAM files, but I'm having a difficult time finding a solution.

I've converted an SRA file to FASTQ with fastq-dump:...
Forum: Bioinformatics 11-18-2014, 10:53 AM
Replies: 1
Views: 1,220
Posted By DPCook
Tools for binning aligned reads?

Hi everyone,

Sorry if the answer exists somewhere, but I have tried searching and have had no luck finding the answer to a possibly naive question.

I'm simply looking for a way to bin aligned...
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