User: Nick N

gravatar for Nick N
Nick N60
Reputation:
60
Status:
Trusted
Location:
United Kingdom
Last seen:
3 years ago
Joined:
4 years, 7 months ago
Email:
f*********@gmail.com

Posts by Nick N

<prev • 20 results • page 1 of 2 • next >
0
votes
1
answers
1.3k
views
1
answers
Comment: C: edgeR/Deseq2 for differential OTU abundance in a mock 16s community?
... The problem is that there is a technical variability between the mock replicates. ps. apologies for posting multiple times the same comment - somehow the submit button did not seem to respond. ...
written 3.0 years ago by Nick N60
0
votes
1
answers
1.3k
views
1
answers
Comment: C: edgeR/Deseq2 for differential OTU abundance in a mock 16s community?
... Yes, the mock community is a sort of spike-in. We were thinking of adding it to each run but we don't know what probabilistic framework to incorporate it. If I remember correctly, there were control probes on the microarrays which could be used for normalisation, We were thinking of using the mock c ...
written 3.0 years ago by Nick N60
2
votes
1
answer
1.3k
views
1
answer
edgeR/Deseq2 for differential OTU abundance in a mock 16s community?
... We have a bacterial mock community consisting of 22 bacterial taxa. The mock community exists in 2 basic versions - one in which each taxon is (supposed to be) equally abundant, and one in which one of the species has inflated abundance (at several different levels).  We would like to use the mock ...
edger deseq2 written 3.0 years ago by Nick N60 • updated 3.0 years ago by Aaron Lun21k
3
votes
2
answers
1.8k
views
2
answers
edgeR: Error in taglist[[i]] : subscript out of bounds
... I have rna-seq data (18 samples) from which I produced the raw counts using htseq-count. Now I want to analyze the data using edgeR. I've done this dozens of times and had no issues. Not this time. When I execute samples <- read.csv(file="metadata_composite.csv",header=TRUE,sep=",") counts < ...
edger rna-seq written 3.2 years ago by Nick N60 • updated 3.2 years ago by Gordon Smyth35k
0
votes
1
answer
970
views
1
answer
Using PCA for unsupervised clustering of RNA-Seq with DESeq2
... I have a set of 96 single-cell RNA-Seq samples. They are all of the same type of cells but I would like to see whether there is any hidden structure in this cell population. I was thinking of performing PCA. I wanted to use DESeq2 but their workflow seems to involve computing the differential expres ...
rnaseq clustering deseq2 pca written 3.4 years ago by Nick N60 • updated 3.4 years ago by Michael Love19k
0
votes
1
answers
871
views
1
answers
Comment: C: How to model a comparison between comparisons in edgeR?
... You are right Aaron - it must have been some sort of code mistake on my part. I couldn't reproduce what I saw before. Thank you very much for your help! ...
written 3.5 years ago by Nick N60
0
votes
1
answers
871
views
1
answers
Comment: C: How to model a comparison between comparisons in edgeR?
... I put the raw counts in a spreadsheet: http://bit.ly/1E4k2KL. Here are the lib sizes and the norm factors: y$samples$lib.size  [1] 29330462 26357396 22566633 28454909 26533897 23963450 33220755 27540983 26982561 31371013 26908984 27572867 21458072 28155268 26135268 34088199 25877118 19837215    &g ...
written 3.5 years ago by Nick N60
0
votes
1
answers
871
views
1
answers
Comment: C: How to model a comparison between comparisons in edgeR?
... Apologies - the actual my.contrast line is: my.contrasts <- makeContrasts(ActivationR71vsActivationR72 = (AR71 - NR71) - (AR72 - NR72)) which doesn't raise an exception. AR71 stands for A.act, NR71 for A.n. AR72 is B.act, NR72 is B.n. I just tried to stick with the original names that I used ...
written 3.5 years ago by Nick N60
0
votes
1
answers
871
views
1
answers
Comment: C: How to model a comparison between comparisons in edgeR?
... Here are the design and contrasts: > design    A.act B.act C.act A.n B.n C.n 1     1    0    0    0    0    0 2     1    0    0    0    0    0 3     1    0    0    0    0    0 4     0    1    0    0    0    0 5     0    1    0    0    0    0 6     0    1    0    0    0    0 7     0    0    1     ...
written 3.5 years ago by Nick N60
0
votes
1
answers
871
views
1
answers
Comment: C: How to model a comparison between comparisons in edgeR?
... I think so. Here is my code: ############################# #read in DGE ############################# d <- readDGE(targets$Files) ############################# #Filter & Library Size Re-set ############################# keep <- rowSums(cpm(d)>1) >=3 d <- d[keep,] d$samples$lib.si ...
written 3.5 years ago by Nick N60

Latest awards to Nick N

Popular Question 3.0 years ago, created a question with more than 1,000 views. For edgeR: Error in taglist[[i]] : subscript out of bounds

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 166 users visited in the last hour