User: Alexander Skates

Reputation:
340
Status:
Trusted
Location:
United Kingdom
Last seen:
2 years, 7 months ago
Joined:
4 years ago
Email:
a***************@googlemail.com

Posts by Alexander Skates

<prev • 37 results • page 1 of 4 • next >
2
votes
1
answer
1.2k
views
1
answers
Answer: A: miRNA differential expression analysis, no significant adjusted p-values
... The issue lay in the fact that the undefined samples acted as noise. Removing all non-epithelial and non-mesenchymal samples gave me better looking results! ...
written 2.7 years ago by Alexander Skates340
3
votes
1
answer
1.2k
views
1
answer
miRNA differential expression analysis, no significant adjusted p-values
... I'm attempting to carry out a differential expression analysis upon a [GEO dataset][1], specifically focusing on the epithelial-mesenchymal transition (EMT). However I've gotten no signifcant results and I don't know where I'm going wrong. I'm using empirical Bayes in limma to identify differential ...
R limma differential expression mirna written 2.7 years ago by Alexander Skates340
1
vote
1
answer
1.3k
views
1
answer
Antibody Structure Prediction
... I'm trying to predict the structure of a monoclonal antibody that does not have a crystal structure (and thus no PDB). I have the sequence for the heavy and light chain, and tried inputting it into Phyre2, but I wasn't sure how to treat the multiple chains. In the end, I just concatenated them both, ...
expasy phyre prediction protein antibody written 3.4 years ago by Alexander Skates340 • updated 3.4 years ago by Sishuo Wang170
1
vote
0
answers
1.3k
views
0
answers
Comment: C: error in rstudio
... If it's a csv file you're loading into a data frame, shouldn't it be sep=","? ...
written 3.7 years ago by Alexander Skates340
0
votes
1
answer
2.7k
views
1
answers
Comment: C: At what point does does a departure from the normal constitute inflation (QQ plo
... That is a fantastic quote. ...
written 3.7 years ago by Alexander Skates340
2
votes
1
answer
2.7k
views
1
answer
At what point does does a departure from the normal constitute inflation (QQ plot)
... I'm trying to interpret a QQ plot I have from Matrix eQTL, to see if there is a factor I haven't accounted for. I know a departure from the x=y at low values can indicate a confounding factor, but at what point is a digression from the normal inflation, and when is it acceptable? Is there a "rule of ...
qq-plot eqtl written 3.7 years ago by Alexander Skates340 • updated 3.7 years ago by Jean-Karim Heriche18k
2
votes
3
answers
6.3k
views
3
answers
Answer: A: How to convert IMPUTE2 to VCF format
... Try QCTOOL. ...
written 3.7 years ago by Alexander Skates340
2
votes
0
answers
1.5k
views
0
answers
Loading IMPUTE2 output into R for eQTL analysis
... I've imputed genome-wide SNPs using the Phase 3 1000 Genomes Project data as a reference set, and I want to use this data to conduct an eQTL analysis. I want to do it in R, owing to the flexibility it affords me, and also the R package Matrix eQTL is supposedly exponentially faster than any other so ...
R imputation eqtl written 3.7 years ago by Alexander Skates340
8
votes
1
answer
3.1k
views
1
answer
Adding text to ideogram in ggbio (or other method recommendations)?
... I have a bed file with the chromosomal coordinates of some snps and their RsIds, e.g. chr1 202187176 202187176 rs6678914 chr14 68660428 68660428 rs2588809 chr6 13722523 13722523 rs204247 chr4 175846426 175846426 rs6828523 chr20 32588095 32588095 rs22843 ...
image ggbio ideogram snp written 3.7 years ago by Alexander Skates340 • updated 22 months ago by bernatgel1.9k
0
votes
2
answers
1.8k
views
2
answers
Answer: A: Reverse gene lookup from SNP
... The R/bioconductor package biomaRt can do this. Look up the associated gene in the hsapiens_snp mart, and then use this in  hsapiens_gene_ensembl to get the gene name. ...
written 3.7 years ago by Alexander Skates340

Latest awards to Alexander Skates

Scholar 2.7 years ago, created an answer that has been accepted. For A: Mapping old Ensembl transcript to a newer one
Scholar 3.8 years ago, created an answer that has been accepted. For A: Mapping old Ensembl transcript to a newer one
Scholar 3.8 years ago, created an answer that has been accepted. For A: Mapping old Ensembl transcript to a newer one
Teacher 3.8 years ago, created an answer with at least 3 up-votes. For A: extracting chip id for a transcription factor
Scholar 3.8 years ago, created an answer that has been accepted. For A: Mapping old Ensembl transcript to a newer one

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 889 users visited in the last hour