User: bryce.kirby

gravatar for bryce.kirby
Reputation:
0
Status:
New User
Last seen:
1 year, 2 months ago
Joined:
1 year, 4 months ago
Email:
b**********@yahoo.com

Profile information, website and location are not shown for new users.

This helps us discourage the inappropriate use of our site.

Posts by bryce.kirby

<prev • 11 results • page 1 of 2 • next >
0
votes
1
answer
641
views
1
answer
Deseq2 Differential Expression (9 samples 3 conditions)
... Hello all, I am using DESeq2 and trying to compare my 3 controls vs. my 3 knockdowns and my 3 controls vs. my 3 overexpressions, Im trying to use the design feature but it isn't giving me the right comparisons. I have my count matrix like this: transcript_id sample1 sample2 sample3 sample4 sam ...
deseq2 rna-seq gsea written 15 months ago by bryce.kirby0 • updated 15 months ago by h.mon26k
0
votes
2
answers
960
views
2
answers
Comment: C: Deseq2 Differentially Expressed Genes between conditions
... Hi thanks for the information! I believe I have made good progress using your help. I have the results from my run using that code, but I'd still like to add which values correspond to which sample. So basically, what would be the best method to add another column that categorizes which sample goes ...
written 15 months ago by bryce.kirby0
3
votes
2
answers
960
views
2
answers
Deseq2 Differentially Expressed Genes between conditions
... Hello friends! I have been working with my RNAseq output after running it thru the Deseq package in R. I have a list "genes.txt" of the genes in my 9 samples, the pvals, log2 fold change etc. I would like to compare lets say: Control vs. Knockdown and then use that input to use for GSEA. Here is ...
R deseq2 rna-seq differential expression gsea written 15 months ago by bryce.kirby0 • updated 15 months ago by Buffo1.6k
3
votes
1
answer
740
views
1
answer
Differential Expression in DEseq2 to GSEA (9 samples, 3 conditions)
... Hello, I am working with RNA-seq data and trying to implement my stringtie output file from "prepDE.py" for all 9 of my samples into DESeq2 to perform differential Expression on my three conditions here is how my data is set up: cell line 1: sample1 (control) sample2 (knockdown) sa ...
stringtie deseq2 rna-seq differential expression written 15 months ago by bryce.kirby0 • updated 15 months ago by Kevin Blighe45k
0
votes
1
answer
2.0k
views
1
answers
Comment: C: Stringtie prepDE.py Error line 32
... Thank you so much!!! Changing the version of python worked! I really appreciate it, this had me stuck for a whole day. ...
written 15 months ago by bryce.kirby0
5
votes
1
answer
2.0k
views
1
answer
Stringtie prepDE.py Error line 32
... Hello, I am working on inputting my data from stringtie -e-B to then perform differential expression on my samples using Deseq. I am running the command 'python prepDE.py -i sample_list.txt' but keep getting this error : python ./prepDE.py -i /scratch/exp_radonc/bkirby/scratch/mazur_lab_scratc ...
stringtie deseq2 ballgown rna-seq prepde.py written 15 months ago by bryce.kirby0 • updated 14 months ago by Biostar ♦♦ 20
0
votes
1
answer
894
views
1
answers
Comment: C: CummeRbund Column Name Mismatch Error
... Hello, I was able to read everything in. I ended up changing the directory to the entire path of where the data was and it worked. Thanks for your help! ...
written 16 months ago by bryce.kirby0
0
votes
1
answer
894
views
1
answers
Comment: C: CummeRbund Column Name Mismatch Error
... Hi I updated everything but not get this error : Creating database RNA-480_Output/cuffData.db Error in rsqlite_connect(dbname, loadable.extensions, flags, vfs) : Could not connect to database: unable to open database file Any ideas? Here is my session info. Thanks so much! > sessionInfo( ...
written 16 months ago by bryce.kirby0
0
votes
0
answers
535
views
0
answers
Cuffdiff genes.fpkm_tracking xloc IDs to Ensembl IDs
... Hello, I am faced with a dilemma, I have run and obtained output from Cuffdiff and was looking to input it into GSEA and CummeRbund, but my gene Ids are Xloc for some reason. For GSEA in particular, I can't run the genes.fpkm_tracking file with the software because there is no available reference b ...
genes.fpkm_tracking ensembl cuffdiff xloc written 16 months ago by bryce.kirby0
0
votes
1
answer
894
views
1
answers
Comment: C: CummeRbund Column Name Mismatch Error
... Sorry for the late reply. Here is my sessionInfo R version 3.4.2 (2017-09-28) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS Sierra 10.12.6 Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS ...
written 16 months ago by bryce.kirby0

Latest awards to bryce.kirby

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1443 users visited in the last hour