User: Sam
Sam • 100
- Reputation:
- 100
- Status:
- Trusted
- Location:
- Last seen:
- 7 hours ago
- Joined:
- 1 year, 4 months ago
- Email:
- V**********@gmail.com
Posts by Sam
<prev
• 146 results •
page 1 of 15 •
next >
0
votes
1
answer
77
views
1
answers
... featurecounts with -g transcript_id give about 20% less DE mRNAs compare to grouping according gene_id. so is it expected to have less DE in transcript level? I think if we compare transcript vs. transcript( for mRNAs vs. lncRNAs transcript correlation), it could produce more robust data. is it tr ...
written 3 days ago by
Sam • 100
1
vote
1
answer
77
views
1
answer
... Dear Biostars
I predicted some lncRNAs transcript according to RNA-seq data and then I used featurecounts to count the lncRNAs transcript (-t exon and -g transcript_id ) in the BAM files. for lncRNA/mRNA co-expression analysis, should I count mRNAs according to transcipt_id or gene_id (-t exon and ...
written 4 days ago by
Sam • 100
2
votes
1
answer
77
views
1
answer
... Dear All
I want use "rcorr.adjust" (https://rdrr.io/cran/RcmdrMisc/man/rcorr.adjust.html)
for gene co-expression analysis but I want to have a the output in one table contain rows , columns name , correlation , P-value and adjust P
any help?
output of rcorr.adjust :
...
0
votes
0
answers
49
views
0
answers
... Dear All
I have a table in this format (sep="\t"):
> head (final_results)
row column cor p
1 Eucgr.A00001.v2.0 Eucgr.A00003.v2.0 0.19259162 0.548714973
2 Eucgr.A00001.v2.0 Eucgr.A00004.v2.0 0.73894587 0.006039257
3 Eucgr.A00003. ...
written 11 days ago by
Sam • 100
0
votes
0
answers
87
views
0
answers
Comment:
C: WGCNA and corAndPvalue
... I think this filter is useful for after getting correlation of genes :) ...
written 11 days ago by
Sam • 100
0
votes
0
answers
87
views
0
answers
Comment:
C: WGCNA and corAndPvalue
... thanks for your reply but I need the gene/gene correlation, should I change my matrix? ...
written 11 days ago by
Sam • 100
1
vote
0
answers
87
views
0
answers
... Hello
for gene-gene pearson correlation analysis with p-value I used this code but it gave me the correlation between samples.
any help about this?
correlation_pvalueDat1=corAndPvalue(data,method="pearson",use="p")
my data format :
Geneid 1-FPKM 2-FPKM 3-FPKM 1-T-GB3-FPKM 1-T-GM58- ...
written 11 days ago by
Sam • 100
0
votes
0
answers
64
views
0
answers
... Dear All
I'm going to use genie3 package for lncRNAs and mRNAs co-expression analysis, can I input just **DE mRNAs and DE lncRNAs** in this package to differential co-expression analysis?
Thanks
...
written 12 days ago by
Sam • 100
3
votes
1
answer
90
views
1
answer
... Hi
I have a expression table in this format
Geneid 1-FPKM 2-FPKM 3-FPKM 1-T-GB3-FPKM 1-T-GM58-FPKM 1-T-MB43-FPKM 34-O-GB3-FPKM 34-O-GM58-FPKM 34-O-MB43-FPKM 34-T-GB3-FPKM 34-T-GM58-FPKM 34-T-MB43-FPKM
A00218.v2.0 0 0 0 0 0 0.090523725 0 0 0 0 0 0
A00223.v2.0 0 ...
written 13 days ago by
Sam • 100
• updated
13 days ago by
finswimmer ♦ 10.0k
0
votes
1
answer
1.3k
views
1
answers
... yes, I have the DE genes, but I think we should not include just DE genes and we need to filter the low expressed ones just according the normalized expression.right? ...
written 13 days ago by
Sam • 100
Latest awards to Sam
Supporter
9 months ago,
voted at least 25 times.
Centurion
10 months ago,
created 100 posts.
Rising Star
15 months ago,
created 50 posts within first three months of joining.
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 1926 users visited in the last hour