User: jma1991

gravatar for jma1991
jma199130
Reputation:
30
Status:
New User
Location:
Last seen:
1 month, 3 weeks ago
Joined:
1 year, 3 months ago
Email:
j******@icloud.com

Posts by jma1991

<prev • 23 results • page 1 of 3 • next >
0
votes
1
answers
170
views
1
answers
Comment: C: Improve limma-voom trend fit to noisy data
... +1 for correcting my misconception, thank you. ...
written 10 weeks ago by jma199130
0
votes
1
answers
170
views
1
answers
Comment: C: Improve limma-voom trend fit to noisy data
... Apologies, I meant X count in *any* N samples, so not filtering based on any group information. That should be independent of the test statistic. You're right about threshold > strategy. I'd like to automate the pre-filtering stage somehow (picking a decent threshold based on the data, HTSFilter ...
written 10 weeks ago by jma199130
0
votes
1
answers
170
views
1
answers
Comment: C: Improve limma-voom trend fit to noisy data
... Thanks for the reply Aaron, I've just double-checked on some colleagues computers, the second image should definitely have the highlighted areas ( https://ibb.co/eEkGqG ) I guess the discreteness issue could be improved by filtering based on X values being in N number of replicates (rather than av ...
written 10 weeks ago by jma199130
4
votes
1
answer
170
views
1
answer
Improve limma-voom trend fit to noisy data
... I'm analysing low cell number ChIP-seq data (3 ChIP replicates / 3 Input replicates). The replicates are highly variable due to the low amount of starting material and the number of PCR cycles used for amplification. I am counting reads into windows along the genome and quantile normalising the coun ...
limma voom written 10 weeks ago by jma199130 • updated 10 weeks ago by Aaron Lun18k
0
votes
1
answers
322
views
1
answers
Comment: C: POU5F1(OCT4) /ENTREZID: 5460 is not in the TxDb.Hsapiens.UCSC.hg19.knownGene
... Sorry, so are you saying OCT4/POU5F1 has transcripts on different chromosomes? ...
written 4 months ago by jma199130
0
votes
1
answers
322
views
1
answers
Comment: C: POU5F1(OCT4) /ENTREZID: 5460 is not in the TxDb.Hsapiens.UCSC.hg19.knownGene
... Actually I'm a bit confused now.. Neither the gene symbol or alias returns the canonical OCT4/POU5F1 gene: library("org.Hs.eg.db") library("TxDb.Hsapiens.UCSC.hg19.knownGene") genes <- genes(TxDb.Hsapiens.UCSC.hg19.knownGene) symbols <- mapIds(org.Hs.eg.db, keys = genes$gene_id, "SYMBOL", k ...
written 4 months ago by jma199130
0
votes
1
answers
322
views
1
answers
Answer: A: POU5F1(OCT4) /ENTREZID: 5460 is not in the TxDb.Hsapiens.UCSC.hg19.knownGene
... It's called POU5F1B instead of POU5F1: library("TxDb.Hsapiens.UCSC.hg19.knownGene") txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene hg19.genes <- genes(txdb) library("AnnotationDbi") library("org.Hs.eg.db") gene_symbol <- AnnotationDbi::select(org.Hs.eg.db, keys=hg19.genes$gene_id, columns=" ...
written 4 months ago by jma199130
0
votes
1
answers
401
views
1
answers
Comment: C: Reads mistakenly being assigned to Unassigned_NoFeatures category when using fea
... Ah that makes sense, thank you for replying ...
written 9 months ago by jma199130
3
votes
1
answer
401
views
1
answer
Reads mistakenly being assigned to Unassigned_NoFeatures category when using featureCounts
... :: I originally posted my question on Biostars, but according to the featureCounts website, I should post on this forum for help :: I am using featureCounts (version 1.5.2) to count the number of reads within bins along the genome: featureCounts -R -F SAF --fracOverlap 1 -Q 1 --primary -T 20 ...
featurecounts subread written 9 months ago by jma199130 • updated 9 months ago by Wei Shi2.7k
0
votes
1
answers
263
views
1
answers
Comment: C: strsplit method for DNAStringSet objects
... That's fantastic, thank you very much. I'll test when it becomes available. ...
written 10 months ago by jma199130

Latest awards to jma1991

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: 267 users visited in the last hour