User: nabiyogesh

gravatar for nabiyogesh
nabiyogesh0
Reputation:
0
Status:
New User
Last seen:
1 day, 17 hours ago
Joined:
2 years, 8 months ago
Email:
n*********@gmail.com

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

This helps us discourage the inappropriate use of our site.

Posts by nabiyogesh

<prev • 33 results • page 1 of 4 • next >
0
votes
0
answers
92
views
0
answers
Comment: C: Phyloseq to metagenomeSeq
... thanks Hector for your all help. obj <- MRcounts(obj, norm = TRUE, log = TRUE). do you also suggest while running MetagenomeSeq should I also use MRcount for normalisation instead of these three line R code: obj = cumNorm(obj, p = cumNormStatFast(obj)) normFactor = normFactors(obj) ...
written 14 days ago by nabiyogesh0
0
votes
0
answers
92
views
0
answers
Comment: C: Phyloseq to metagenomeSeq
... Dear Hector, Thanks for your response, I also want to compare abundant ASV from metagenomeSeq with normalized ASV count, for that should I use output from below command, will it give me normalized ASV count? and then I want to convert it into log2 value and can cross check the metagenomeSeq resul ...
written 16 days ago by nabiyogesh0
0
votes
1
answer
52
views
1
answers
Comment: C: phyloseq to edgeR
... Thanks a lot Smyth. I just want to add one more thing that these treatment were collected from 9 different locations so to ignore the location effect do I need to change group formula to location + Treatment? location is also a part of metadata column as like treatment. and then can I use the the ...
written 16 days ago by nabiyogesh0
0
votes
1
answer
52
views
1
answer
phyloseq to edgeR
... Hi, I do have three treatment condition (T1, T2 and T3), could you please suggest how I can improve below code to extract pairwise comparisons in edgeR after importing data from phyloseq object to edgeR. dge = phyloseq_to_edgeR(kosticB, group="Treatment") # Perform binary test et = ex ...
edger written 20 days ago by nabiyogesh0 • updated 20 days ago by Gordon Smyth37k
0
votes
0
answers
92
views
0
answers
Comment: C: Phyloseq to metagenomeSeq
... Thanks Hector, do you mean I should use this command like below: settings = zigControl() thanks for your time and help. nabiyogesh ...
written 20 days ago by nabiyogesh0
0
votes
0
answers
92
views
0
answers
Comment: C: Phyloseq to metagenomeSeq
... Thank you very much for your response. I have not done normalization in phyloseq so I am doing it with below commands in metagenomeSeq, here I used maxit =10, could you please suggest to help me to understand the maxit value, how should I know whether I am using correct maxit value or not? #cal ...
written 26 days ago by nabiyogesh0
0
votes
0
answers
92
views
0
answers
Phyloseq to metagenomeSeq
... Hi, I am new to R and trying to understand metagenomeSeq, I will be very much thankful if you could help me to understand this: I do have three treatment condition (T1, T2, and T3) and want to see how these treatments affect the microbial diversity in rice roots. I am interested in the pairwise co ...
limma metagenomeseq written 5 weeks ago by nabiyogesh0
0
votes
1
answer
55
views
1
answer
Phylpseq to deseq2
... Hi Michael, I do have three treatment: T1, T2 and T3: I am interested in all three pairwise comparisons. For that Should I need to make one of them as a reference or by using contrast I can get all three comparisons? If I extract logfold change in below comparison what does it means: ...
deseq2 written 5 weeks ago by nabiyogesh0 • updated 5 weeks ago by Michael Love24k
0
votes
1
answer
93
views
1
answers
Comment: C: DESeq not showing all coefficient
... Dear Michael, could you please confirm me in above comparison which is act as a reference. How the reference is decided in these cases where we group two variable. If extract two fold up and down log2fold change result from the below code then what does it mean: geno_stage_HRPR_12D_vs_HRPR_0D ...
written 5 weeks ago by nabiyogesh0
0
votes
1
answer
93
views
1
answers
Comment: C: DESeq not showing all coefficient
... Thank a lot, Michael. I do have one more query: To extract differential expressed genes which output we used from below these two command: **res <- results(dds, name="condition_trt_vs_untrt")** # or to shrink log fold changes association with condition: **res <- lfcShrink(dds, c ...
written 6 weeks ago by nabiyogesh0

Latest awards to nabiyogesh

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 16.09
Traffic: 271 users visited in the last hour