User: Biogeek

gravatar for Biogeek
Biogeek260
Reputation:
260
Status:
Trusted
Location:
Last seen:
2 months, 3 weeks ago
Joined:
4 years, 1 month ago
Email:
p**********@gmail.com

about me

Posts by Biogeek

<prev • 143 results • page 1 of 15 • next >
0
votes
2
answers
272
views
2
answers
Comment: C: Heatmap.2 - flip dendrogram so control group appears on LHS?
... Sorry for being ignorant. I'm unsure how I can feed the above hclustfun into my code. Can you explain how I incorporate that into heatmap.2(....)?Thanks. ...
written 12 weeks ago by Biogeek260
0
votes
2
answers
272
views
2
answers
Comment: C: Heatmap.2 - flip dendrogram so control group appears on LHS?
... heatmap.2(lc2, col=colfunc(200),Colv= F, main = "Sample",dendrogram = "both", scale = "none", trace = "none", keysize = 1.0, key.ylab = NA, density.info = "none",key.xlab = "Z-score", labRow = "", breaks = seq(-2, 2, length.out = 201))) My code above, is there a way to do this in that? I'm just usi ...
written 12 weeks ago by Biogeek260
0
votes
2
answers
272
views
2
answers
Comment: C: Heatmap.2 - flip dendrogram so control group appears on LHS?
... I will see what I can do. Would it matter if I didn't provide the top dendrogram (Vcol = FALSE) . That command allows me to have control on LHS but just no dendrogram. ...
written 12 weeks ago by Biogeek260
0
votes
2
answers
272
views
2
answers
Comment: C: Heatmap.2 - flip dendrogram so control group appears on LHS?
... Have tried these methods, but no luck, Them methods seem to only adjust the rows around? The closest I have got is feeding Vcol = (4,5,6,1,2,3), however, the upper dendrogram becomes flat and doesn't offer any insight into similarity of samples. ...
written 12 weeks ago by Biogeek260
0
votes
2
answers
272
views
2
answers
Comment: C: Heatmap.2 - flip dendrogram so control group appears on LHS?
... Hey mate, I tried Colv but it omits the upset dendogram. Would prefer to keep it o show the distances/ similarity. When you say feed it a vector can you elaborate? I give heatmap.2 a matrix of values. Even if I reorder the matrix columns, it still puts the heatmap as is. 😞 ...
written 12 weeks ago by Biogeek260
4
votes
2
answers
272
views
2
answers
Heatmap.2 - flip dendrogram so control group appears on LHS?
... I am wanting to flip the dendrogram above my heatmap so that the SC group appears on the left of the heatmap and the IO group appears on the right as opposed to the left. Is there anyway I can do this without removing the dendrograms? The SC is the control group and as such it seems logical that it ...
R heatmap written 12 weeks ago by Biogeek260 • updated 12 weeks ago by e.rempel540
0
votes
1
answer
423
views
1
answer
Easier way to filter contaminants based on protein similarity ?
... Hey guys, I'm familiar with the idea of blob plots, but for filtering off contaminants in a plant I've sequenced. I've so far used a manual screening protocol, whereby I take the top hit of each query ( sim identity , but score and e value) . I then use the uniprot and trembl species identifiers to ...
trembl blastx diamond uniprot written 14 months ago by Biogeek260 • updated 14 months ago by Elisabeth Gasteiger1.3k
0
votes
0
answers
396
views
0
answers
Comment: C: weird e-values with rapsearch
... may i add... the sequences with these values are rather large. i.e +10k bp in size. ...
written 15 months ago by Biogeek260
0
votes
0
answers
396
views
0
answers
weird e-values with rapsearch
... Hi, I've used RAPsearch2 in -s F mode, which equates to NCBI blastX e-value output style. I have used a threshold of 0.00001. 1x10-5..some of my blast hits I get are as follows: I'm getting e values which start as -(number)e+08. Usually I get e-values of ( number)e-(number). Stupid question but -3 ...
rapsearch e-values written 15 months ago by Biogeek260
0
votes
1
answer
292
views
1
answers
Comment: C: swiss-prot size reduction
... uniprot taxonomic divisions, look for the viridiplantae or plants datasets. Depending on the environment your plant came from, you may also be more beneficial using the complete uniprot database as I know from my experience in working with plant seq data, we get a lot of fungal and bacterial conta ...
written 15 months ago by Biogeek260

Latest awards to Biogeek

Great Question 14 months ago, created a question with more than 5,000 views. For MDS plots with R
Epic Question 14 months ago, created a question with more than 10,000 views. For MDS plots with R
Popular Question 14 months ago, created a question with more than 1,000 views. For Can you pool individuals to make 1 biological replicate?
Popular Question 14 months ago, created a question with more than 1,000 views. For MDS plots with R
Popular Question 15 months ago, created a question with more than 1,000 views. For FPKM values / Data analysis
Centurion 17 months ago, created 100 posts.
Scholar 21 months ago, created an answer that has been accepted. For A: Visualize groups of conditions bys MDS.
Student 22 months ago, asked a question with at least 3 up-votes. For Filtering by FPKM, opinions and thoughts
Great Question 22 months ago, created a question with more than 5,000 views. For MDS plots with R
Popular Question 3.6 years ago, created a question with more than 1,000 views. For FPKM values / Data analysis
Popular Question 3.6 years ago, created a question with more than 1,000 views. For Trinity/Rsem/Edger Pipeline...Now What?
Popular Question 3.6 years ago, created a question with more than 1,000 views. For MDS plots with R
Popular Question 3.6 years ago, created a question with more than 1,000 views. For normalized FPKM matrix file EdgeR and GO Mapping

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 611 users visited in the last hour