User: agdif

gravatar for agdif
agdif0
Reputation:
0
Status:
New User
Last seen:
6 days, 5 hours ago
Joined:
7 months, 3 weeks ago
Email:
c*****@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 agdif

<prev • 5 results • page 1 of 1 • next >
0
votes
0
answers
107
views
0
answers
DESeq2: Extract mean normalized log2 counts by level
... Hi, I currently am using a dataset with 5 timepoints and 4 replicates per timepoint. While the results file exports the L2FC, I am also interested in extracting the numerator log2 values for each time point. I have already extracted the log2 normalized counts for each individual sample with the cod ...
log2 normalized counts written 4 months ago by agdif0
0
votes
1
answer
147
views
1
answer
DESeq2: likelihood ratio test interpretation, multifactor
... Hi Michael, I would like to make sure that I am interpretating the p-values correctly when using the likelihood ratio test with a multifactor design. We are interested in identifying significant genes that are differentially expressed between 3 disease states while controlling for sex. I understan ...
deseq2 lrt likelihood ratio test written 5 months ago by agdif0 • updated 5 months ago by Michael Love21k
1
vote
1
answer
141
views
1
answer
biomaRt getBM() function does not recognize gene ID character vector values generated from csv file for annotation
... I have a multi-column csv file. In the first column are ensembl IDs that I would like to annotate using biomaRt in RStudio. After reading the csv file into R as a dataframe I have converted the first column with the IDs to a character vector, since the getBM() parameter, values, requires a list of ...
annotation biomart ensembl csv files getbm() written 6 months ago by agdif0 • updated 6 months ago by Mike Smith3.2k
0
votes
1
answer
202
views
1
answers
Comment: C: Better to use rlog or vst transformation for data quality assessment of differen
... Thanks Michael!  ...
written 7 months ago by agdif0
2
votes
1
answer
202
views
1
answer
Better to use rlog or vst transformation for data quality assessment of differental expression data based on size factors?
... Hello, I finished running DESeq2 on my dataset that includes 6 timepoints and 3 biological replicates per timepoint. I would like to run a PCA analysis for quality assessment but am unsure which count transformation method I should use, vst or rlog.  The calculated the size factors for my dataset ...
deseq2 rlog transformation vst quality assesment written 7 months ago by agdif0 • updated 7 months ago by Michael Love21k

Latest awards to agdif

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: 209 users visited in the last hour