User: pvd2107

gravatar for pvd2107
pvd21070
Reputation:
0
Status:
New User
Location:
Last seen:
1 month ago
Joined:
7 months, 3 weeks ago
Email:
p******@cumc.columbia.edu

Posts by pvd2107

<prev • 8 results • page 1 of 1 • next >
0
votes
2
answers
899
views
2
answers
Comment: C: DESeq2 resultsNames(dds) not giving the right comparisons?.
... I have a related question. I initially ran lfcShrink on my DESeq dataset using contrast to look at specific pairwise comparisons. Ex: YCNTvsYHET <- lfcShrink(dds_DESeq, contrast = c("group","YCNT", "YHET"), alpha = 0.05, lfcThreshold = 1) I'm interested in using the apeglm shrinkage approach si ...
written 4 weeks ago by pvd21070
0
votes
1
answers
184
views
1
answers
Comment: C: Selecting Correct Set of Gene IDs from Mouse Gencode GFF3 for RNA Seq Analysis (
... Thanks a lot Michael, great to know that this is common practice to include all the genes from the annotation. lfcShrink definitely helps to moderate the LFC values, especially for these low count genes from certain groups. Seems like this will be more appropriate as an input to GSEA, etc.  ...
written 6 months ago by pvd21070
0
votes
1
answers
184
views
1
answers
Comment: A: Selecting Correct Set of Gene IDs from Mouse Gencode GFF3 for RNA Seq Analysis (
... I've also noted that Gencode offers a protein coding transcript sequences fasta file. I could alternatively make an index from this file and run Salmon, which seems like it would get around my issue. I've seen this in the methods section of a few papers I've read, so maybe that is the best approach ...
written 6 months ago by pvd21070
1
vote
1
answer
184
views
1
answer
Selecting Correct Set of Gene IDs from Mouse Gencode GFF3 for RNA Seq Analysis (Removing Genes without symbols)
... Hi, I apologize if the answer to this question is obvious or located elsewhere, but I spent quite a bit of time searching online and posts on this site for an answer with no luck and I've been stuck on it for several days. I am in the process of an RNA-seq analysis using the Salmon -> Tximport - ...
deseq2 org.mm.eg.db gencode tximport written 6 months ago by pvd21070
0
votes
1
answers
140
views
1
answers
Comment: C: DESeq2 - Effect of DDS Import of All vs Select Conditions
... sorry about that, thanks! ...
written 7 months ago by pvd21070
1
vote
1
answer
140
views
1
answer
DESeq2 - Effect of DDS Import of All vs Select Conditions
... Hi Everyone, We've recently completed an RNASeq experiment with 35 samples and 10 different conditions. Almost all of our biological questions are about pairwise comparisons between two of these conditions.  As of now, my workflow has been to import all of the samples as follows: dds <- DESeq ...
deseq2 written 7 months ago by pvd21070 • updated 7 months ago by Michael Love19k
0
votes
1
answers
1.0k
views
1
answers
Comment: C: Constructing tx2gene for Salmon txImport Quantification using Gencode Mouse Tran
... Got it, I think this is definitely where my issue is coming from. Below is a head of the first few transcript quantifications. The first part, the transcript name, is identical to the TXNAME in tx2gene. It's just that it also seems to have a lot of additional gene level inforamtion delimited by |. I ...
written 7 months ago by pvd21070
5
votes
1
answer
1.0k
views
1
answer
Constructing tx2gene for Salmon txImport Quantification using Gencode Mouse Transcript Annotation
... Hi, This question is in reference to the recently updated TxImport vignette: https://bioconductor.org/packages/3.7/bioc/vignettes/tximport/inst/doc/tximport.html  I saw a related question from a few months back but wasn't able to follow the solution and am posting again, thanks in advance. I ran ...
salmon tximport michael love tx2gene written 7 months ago by pvd21070 • updated 7 months ago by Michael Love19k

Latest awards to pvd2107

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: 202 users visited in the last hour