User: CC

gravatar for CC
CC10
Reputation:
10
Status:
New User
Location:
United States
Last seen:
9 months ago
Joined:
3 years, 2 months ago
Email:
h******@gmail.com

Posts by CC

<prev • 11 results • page 1 of 2 • next >
0
votes
1
answers
350
views
1
answers
Comment: C: Details of gene names in DE
... I figured it out, posting here for anyone that might find it useful: > keggs <- select(org.Hs.eg.db, z[[1]], "PATH") > firstkeggs <- subset(keggs, PATH %in% "04614") > firstkeggs$SYMBOL <- mapIds(org.Hs.eg.db, as.character(firstkeggs$ENTREZID), "SYMBOL","ENTREZID") ...
written 9 months ago by CC10
0
votes
1
answers
350
views
1
answers
Comment: C: Details of gene names in DE
... This was incredibly helpful for me, thank you.  How would you perform the same type of extraction for genes in the topKEGG pathways? Thank you in advance! ...
written 9 months ago by CC10
0
votes
4
answers
1.5k
views
4
answers
Answer: A: Running Combat in SVA with NA values in matrix
... This is incredibly helpful, many thanks to you both.  ...
written 3.0 years ago by CC10
3
votes
4
answers
1.5k
views
4
answers
Running Combat in SVA with NA values in matrix
... Hi there,  I ran Combat on 450k data for ~3000 samples and was pleased with the results. However, in order to get the script to run I had to omit any probes with NA values for any sample from the dataset. Due to this, if I want to use the Combat adjusted values for my downstream analysis, I will lo ...
sva combat written 3.0 years ago by CC10
0
votes
1
answers
1.2k
views
1
answers
Comment: C: Loading beta values into minfi
... Okay, thank you, that makes sense. I appreciate your assistance. ...
written 3.1 years ago by CC10
0
votes
1
answers
1.2k
views
1
answers
Comment: C: Loading beta values into minfi
... Just beta values unfortunately. ...
written 3.1 years ago by CC10
0
votes
1
answers
1.2k
views
1
answers
Comment: C: Loading beta values into minfi
... Hi Kasper,  I was able to load the data into a GenomicRatioSet using your advice. However, when I run GetSex, I get the following error - presumably because I do not have CN values available to me. Is there a way around this? > Error in .getSex(CN = CN, xIndex = xIndex, yIndex = yIndex, cutoff ...
written 3.1 years ago by CC10
0
votes
1
answers
1.2k
views
1
answers
Comment: C: Loading beta values into minfi
... Thank you so much for your fast and very helpful reply. ...
written 3.1 years ago by CC10
1
vote
1
answer
1.2k
views
1
answer
Loading beta values into minfi
... Hi there,  I have only beta values available to me in a matrix from 450k array data. I am trying to load the values into minfi as a GenomicRatioSet but keep getting the same error: > ratioSet <- ratioConvert(betaM, what="beta", keepCN=TRUE) > Error in (function (classes, fdef, mtable)  : ...
minfi 450k written 3.1 years ago by CC10 • updated 3.1 years ago by Kasper Daniel Hansen6.4k
0
votes
1
answers
759
views
1
answers
Comment: C: Loading RData files into ChAMP
... Hi there, thank you for your response. I suppose the issue is that it is not in the right format as when I load the RData file, the ChAMP commands will not work. I am sorry to ask such a basic question but I cannot seem to figure out what the right format is for the ChAMP functions from any of the p ...
written 3.2 years ago by CC10

Latest awards to CC

Popular Question 2.9 years ago, created a question with more than 1,000 views. For Running Combat in SVA with NA values in matrix

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 245 users visited in the last hour