SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 11 of 11
Search took 0.00 seconds.
Search: Posts Made By: KellerMac
Forum: Bioinformatics 09-04-2015, 11:48 AM
Replies: 1
Views: 557
Posted By KellerMac
Sorting VCFs from INFO field

VCFs have an INFO column that contains many sub-categories, depending on the annotations available at the time of calling. Is there a method of sorting VCFs using the sub field info? This would seem...
Forum: Bioinformatics 08-14-2014, 02:24 PM
Replies: 2
Views: 934
Posted By KellerMac
I found a post on BioStar that suggested using...

I found a post on BioStar that suggested using BEDOPS to convert to the more common BED file and proceed in analysis from there.
Forum: Bioinformatics 08-14-2014, 01:26 PM
Replies: 2
Views: 934
Posted By KellerMac
RNAseq .wig files

Hello all! I need to analyze some RNAseq data in .wig (wiggle) format, that I obtained from a paper, but I am unfamiliar with this format. I want to filter for a certian set of genes (ovary related)...
Forum: Site Announcements 06-27-2014, 06:09 AM
Replies: 4
Views: 47,075
Posted By KellerMac
Thank you

Ah I was wondering what was going on with the site! Glad it's not just me! I wanted to take this opportunity to THANK YOU for running the forum it has been a great help to me over the years. There...
Forum: Bioinformatics 07-06-2011, 09:28 AM
Replies: 13
Views: 5,698
Posted By KellerMac
Do I need to delete the older version of DESeq?...

Do I need to delete the older version of DESeq? If so where do you think it would be?
Forum: Bioinformatics 07-05-2011, 02:00 PM
Replies: 13
Views: 5,698
Posted By KellerMac
Variance Estimation

I have been using DESeq to analyze gene expression from SAGE samples. To decide how to compare samples we have been using ECDF (empirical cumulative data function) plots to determine the quality of...
Forum: Bioinformatics 06-10-2011, 10:27 AM
Replies: 3
Views: 3,476
Posted By KellerMac
Thanks For the quick reply Mr. Black Ok, I...

Thanks For the quick reply Mr. Black

Ok, I understand that the data can be sorted manually in excel, but I don't see what corelation is among the genes that are marked as differential expressed. I...
Forum: Bioinformatics 06-10-2011, 07:49 AM
Replies: 3
Views: 3,476
Posted By KellerMac
DESeq DiffExpress Vs. Fold Change

I don't understand the logic behind the data set DESeq provides when I perform the differential expression command. All of the numbers in the columns are in random order, there is not one column that...
Forum: Introductions 06-10-2011, 07:40 AM
Replies: 3
Views: 1,278
Posted By KellerMac
start out with section two "preparations" and...

start out with section two "preparations" and import your data from a text or exel file into "r" it can be a little tricky my command looked like this exampleFile =...
Forum: Introductions 06-09-2011, 07:17 AM
Replies: 3
Views: 1,278
Posted By KellerMac
On the bioconductor webpage there is a pdf file...

On the bioconductor webpage there is a pdf file you can download that runs through analyzing data with deseq. Its not that hard, and you can copy and paste commands directly from the pdf to the R...
Forum: Bioinformatics 06-03-2011, 10:41 AM
Replies: 39
Views: 18,699
Posted By KellerMac
Viewing processed data

Great program for processing data. I used it to find fold change and which genes had the greatest fold change between groups. I want to know if its possible to sort the data according to fold change...
Showing results 1 to 11 of 11

 


All times are GMT -8. The time now is 06:31 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO