User: rmf

gravatar for rmf
rmf0
Reputation:
0
Status:
New User
Location:
Last seen:
1 month, 3 weeks ago
Joined:
4 months ago
Email:
r***************@gmail.com

Posts by rmf

<prev • 5 results • page 1 of 1 • next >
0
votes
0
answers
95
views
0
answers
DEXSeq Count files do not correspond to the flattened annotation file
... Enter your post below.  Please format any code samples that are included in your question. Information about formatting your code can be found on the F.A.Q. page.Enter your post below.  Please format any code samples that are included in your question. Information about formatting your code can be f ...
dexseq R written 9 weeks ago by rmf0
0
votes
1
answers
167
views
1
answers
Comment: C: RNA-Seq Batch correction negative values
... My thinking was that I would batch correct the raw counts to get corrected raw counts which would be used in DESeq2 along with the model (which would now exclude the corrected batch variable). What kind of counts do you think the correction should be applied on? It cannot be log-cpm, vst, rlog, voom ...
written 11 weeks ago by rmf0
0
votes
1
answers
167
views
1
answers
Comment: C: RNA-Seq Batch correction negative values
... Ahan. So batch effect correction works only if all the samples in that batch are affected and not partially? By fixing the negative values, I meant to say to make them all positive because counts cannot be negative. And negative counts cannot be used by DGE packages. Anywya, I will try sva. Thanks f ...
written 11 weeks ago by rmf0
0
votes
1
answer
167
views
1
answer
RNA-Seq Batch correction negative values
... In my bulk RNA-seq dataset, I noticed a few outliers on MDS plot and on further investigation found that these samples originated from one extraction batch (extbatch) 7.  Fig 1: MDS plot showing outliers and that they belong to extbatch 7. Most of the samples from batch 7 and even batch 8 had lo ...
sva combat rna-seq scran batch-effect written 11 weeks ago by rmf0 • updated 11 weeks ago by Aaron Lun17k
1
vote
1
answer
441
views
1
answer
Does SC3 correct counts for gene length?
... Hi, I am interesting in clustering my single cell data to identify clusters and then figure out if certain genes differ in expression profiles and then try to link them to developmental stages.  1. So, to be able to compare gene to gene expression, I suppose the expression scores should be correct ...
rna-seq single-cell scater sc3 biclustering written 4 months ago by rmf0 • updated 3 months ago by Vladimir Kiselev130

Latest awards to rmf

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: 154 users visited in the last hour