User: hs.lansdell

gravatar for hs.lansdell
hs.lansdell10
Reputation:
10
Status:
New User
Location:
Last seen:
6 months ago
Joined:
8 months ago
Email:
h**********@gmail.com

Posts by hs.lansdell

<prev • 21 results • page 1 of 3 • next >
0
votes
1
answers
164
views
1
answers
Comment: C: Missing condition information from colData in DESeq2 gives enormous False Positi
... I did remove the samples for actual analysis. I just wanted an explanation for why it drove up the number of deferentially expressed genes, which you answered, thanks very much!  ...
written 6 months ago by hs.lansdell10
0
votes
1
answers
164
views
1
answers
Comment: C: Missing condition information from colData in DESeq2 gives enormous False Positi
... So the top is just my count matrix. I had a few samples at the bottom that had a sample name, but no value in the actual column under 'condition. The results table was just the first:  res <- results(dds) ...
written 6 months ago by hs.lansdell10
0
votes
1
answer
164
views
1
answer
Missing condition information from colData in DESeq2 gives enormous False Positives?
... Hello! So, I ran DESeq2 against female rna seq data with a dichotomous outcome ('yes', 'no'). I discovered, that some of my sample at the end had no value listed for condition, i.e: 10XXX yes 59XX no XX13 no 8XX7   1XXX9   96XX ...
deseq2 written 6 months ago by hs.lansdell10 • updated 6 months ago by Michael Love18k
0
votes
1
answers
192
views
1
answers
Comment: A: contamination and DESeq2 performance
... Thanks for that! The plot looks very strange..https://ibb.co/gARrh6 ...
written 6 months ago by hs.lansdell10
0
votes
1
answers
137
views
1
answers
Comment: C: DESeq2 76% of genes labeled 'low count'
... Thanks for looking! ...
written 6 months ago by hs.lansdell10
0
votes
1
answers
137
views
1
answers
Comment: C: DESeq2 76% of genes labeled 'low count'
... R version 3.4.2 (2017-09-28) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows >= 8 x64 (build 9200) Matrix products: default locale: [1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C    LC_ ...
written 6 months ago by hs.lansdell10
0
votes
1
answer
137
views
1
answer
DESeq2 76% of genes labeled 'low count'
... Hello! I am running DESeq2 on a dichotomous outcome (77 no, 41 yes). My concern, is that I am getting an enormous number of counts labeled as low. I've been using the same count matrix for other runs, just pulling the samples I need for the process (which I get. changes the matrix depending on whic ...
deseq2 low count genes written 6 months ago by hs.lansdell10 • updated 6 months ago by Michael Love18k
0
votes
1
answer
142
views
1
answer
Running DESeq2 on top variable genes?
... Since looking at the row variance and DESeq2 both act as ranking mechanisms for genes, is there any sense to taking the top 1000 or 5000 genes with the highest variance across samples from an RNA sequenced set and running the DESeq2 pipeline on that subset to look for differential genes between grou ...
deseq2 genes variance written 7 months ago by hs.lansdell10 • updated 7 months ago by Michael Love18k
0
votes
2
answers
218
views
2
answers
Comment: C: Design model for DESeq2 analysis
... Thank you! I'm trying this now!   ...
written 7 months ago by hs.lansdell10
0
votes
2
answers
218
views
2
answers
Comment: C: Design model for DESeq2 analysis
... Thanks for the input! ...
written 7 months ago by hs.lansdell10

Latest awards to hs.lansdell

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 2.2.0
Traffic: 125 users visited in the last hour