User: Sam

gravatar for Sam
Sam100
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
Comment: C: featurecounts flags for lncRNA and mRNA co-expression
... 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 Sam100
1
vote
1
answer
77
views
1
answer
featurecounts flags for lncRNA and mRNA co-expression
... 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 ...
co-expression featurecounts written 4 days ago by Sam100
2
votes
1
answer
77
views
1
answer
co-expression output format(rcorr.adjust)
... 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 : ...
R co-expression written 8 days ago by Sam100 • updated 8 days ago by zx87546.5k
0
votes
0
answers
49
views
0
answers
(Closed) retrieve lines with bash/awk
... 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. ...
awk bash written 11 days ago by Sam100
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 Sam100
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 Sam100
1
vote
0
answers
87
views
0
answers
WGCNA and corAndPvalue
... 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- ...
wgcna written 11 days ago by Sam100
0
votes
0
answers
64
views
0
answers
genie3 for lncRNAs and mRNAs co-expression
... 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 ...
genie3 differential co-expression analysis written 12 days ago by Sam100
3
votes
1
answer
90
views
1
answer
filter gene expression matrix
... 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 ...
filter gene expression written 13 days ago by Sam100 • updated 13 days ago by finswimmer10.0k
0
votes
1
answer
1.3k
views
1
answers
Comment: C: Construct gene coexpression network
... 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 Sam100

Latest awards to Sam

Popular Question 6 months ago, created a question with more than 1,000 views. For bash and awk code
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.

Help
Access

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