## User: Peter

Peter0
Reputation:
0
Status:
New User
Location:
United Kingdom
Last seen:
7 months, 2 weeks ago
Joined:
2 years, 3 months ago
Email:
p*********@ncl.ac.uk

#### Posts by Peter

<prev • 6 results • page 1 of 1 • next >
0
276
views
0
... Assuming your question is "is it OK to have different number of control / treatment replicates", then the answer is yes, it is OK. Is the badly prepared control library the same as the one that plots with the treatments? Could you provide more detail, such as the technique used (RNA-seq?) or the R ...
written 23 months ago by Peter0
1
479
views
1
... Using the guide then it would look like this: ... y <- DGEList(cts) keep <- rowSums(cpm(y) > 2) >= 3 y <- y[keep, , keep.lib.sizes=FALSE] But then I guess I need to recalculate the normalization factors, and also was not sure about the offset calculation. y$offset <- t(t(log(n ... written 2.0 years ago by Peter0 1 answer 479 views 1 answer ... The tximport vignette describes the following steps for using the data with edgeR: https://github.com/mikelove/tximport/blob/master/vignettes/tximport.md library(edgeR) cts <- txi$counts normMat <- txi\$length normMat <- normMat/exp(rowMeans(log(normMat))) library(edgeR) o <- log(calcN ...
written 2.0 years ago by Peter0 • updated 2.0 years ago by Michael Love19k
1
1.7k
views
1
Comment: C: Trouble with Tximport
... I get the same error when using Gencode fasta files with salmon, because the quant.sf output becomes: Name Length EffectiveLength TPM NumReads ENST00000456328.2|ENSG00000223972.5|OTTHUMG00000000961.2|OTTHUMT00000362751.1|DDX11L1-002|DDX11L1|1657|processed_transcript| 1657 1456.57 ...
written 2.0 years ago by Peter0
2
367
views
2
... Thank you for the comment, it's true that there are two rounds of error, although I think a more profound loss arises from not including the genes that are not DE against both controls. Also yes, there is the danger that the intersect approach ignores effects countering the placebo effect. However, ...
written 2.2 years ago by Peter0
2
367
views
2
... I have RNA-seq data from a 3-level 1-factorial experiment: non-treated control, placebo-treated negative control, and treated cells. I have 3 replicates for each. After running edgeR, and also looking at expression levels, I noticed that the negative control is not a good control, as it has DE gene ...
written 2.3 years ago by Peter0 • updated 2.2 years ago by Gavin Kelly560

#### Latest awards to Peter

No awards yet. Soon to come :-)

Content
Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.