User: e.rempel

gravatar for e.rempel
e.rempel540
Reputation:
540
Status:
Trusted
Location:
Germany, Heidelberg, COS
Last seen:
24 minutes ago
Joined:
2 years, 7 months ago
Email:
e*******@dkfz-heidelberg.de

Statistician/bioinformatician.

Posts by e.rempel

<prev • 78 results • page 1 of 8 • next >
0
votes
3
answers
134
views
3
answers
Answer: A: Set multiple attributes to a single node in R
... Hi, is it a `data.frame`? I am asking because you said > I have a list of genes If it is a data.frame, you could just remove `[1]` from genes <- genes[!duplicated(genes[1]),] because `duplicated` can work on rows. ...
written 28 days ago by e.rempel540
0
votes
2
answers
200
views
2
answers
Answer: A: Heatmap.2 - flip dendrogram so control group appears on LHS?
... Hi, Kevin already posted about `reorder` function. In my previous [answer][1] I provided one example how to choose weights for specific branches in dendrogram. [1]: https://www.biostars.org/p/237067/#247980 ...
written 28 days ago by e.rempel540
0
votes
0
answers
183
views
0
answers
Comment: C: Heatmap with contour and numbers
... Honestly, I don't really understand the plot, much less explain how you could do something similar in R/Python. ...
written 29 days ago by e.rempel540
0
votes
1
answer
88
views
1
answers
Comment: C: Manhattan plot in r
... Does it work if you copy-paste 3 lines? ...
written 29 days ago by e.rempel540
0
votes
1
answer
88
views
1
answers
Answer: A: Manhattan plot in r
... *i* is a variable, not a character. Remove the quotation marks. ...
written 29 days ago by e.rempel540
0
votes
1
answer
148
views
1
answers
Comment: C: gene expression variance equality
... May I ask why? *limma* and other tools inherit the "good" properties of t-Test and have some additional advantages. Personally, I would use t-Test in case of (real) many replicates and a few genes. ...
written 29 days ago by e.rempel540
0
votes
1
answer
175
views
1
answers
Comment: C: How to generate a ROC curve for a dataset?
... I think this question should be asked on [StackOverflow][1]. [1]: https://stackoverflow.com/ ...
written 4 weeks ago by e.rempel540
1
vote
1
answer
147
views
1
answers
Answer: A: Generating heatmaps of pre-selected candidate genes after deseq2
... Hi, it is absolutely possible. Have a look at this [tutorial][1]. You could slice the matrix of normalized counts to contain only *interesting genes*: pheatmap(assay(ntd)[intersting_genes,], cluster_rows=FALSE, show_rownames=FALSE, cluster_cols=FALSE, annotation_col=df) [1]: http: ...
written 4 weeks ago by e.rempel540
1
vote
1
answer
148
views
1
answers
Answer: A: gene expression variance equality
... Hi, citation from this [thread][1] (answer from [Gordon Smyth][2] - author of limma): > Unequal variances are not usually a major concern in microarray data. The two-sample t-test is known to be highly robust against unequal variances, and the limma moderated t-test inherits this property. Thu ...
written 4 weeks ago by e.rempel540
0
votes
1
answer
127
views
1
answers
Answer: A: how to normalize microarray expression set
... Hi, the error message resembles one in this [thread][1]. It looks like you should use *different* **rma** function, namely from **oligo** package. You could try `oligo::rma` instead of `rma` (after possible installation of `oligo` library) [1]: https://support.bioconductor.org/p/71097/ ...
written 4 weeks ago by e.rempel540

Latest awards to e.rempel

Scholar 7 days ago, created an answer that has been accepted. For A: GO analysis using topGO Arabidopsis
Appreciated 9 weeks ago, created a post with more than 5 votes. For A: GO analysis using topGO Arabidopsis
Scholar 9 weeks ago, created an answer that has been accepted. For A: GO analysis using topGO Arabidopsis
Scholar 9 weeks ago, created an answer that has been accepted. For A: Heatmap.2 giving specific color to a value and start gradient after
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: GO analysis using topGO Arabidopsis
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: GO analysis using topGO Arabidopsis
Supporter 3 months ago, voted at least 25 times.
Scholar 3 months ago, created an answer that has been accepted. For A: GO analysis using topGO Arabidopsis
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: GO analysis using topGO Arabidopsis
Scholar 3 months ago, created an answer that has been accepted. For A: GO analysis using topGO Arabidopsis
Scholar 3 months ago, created an answer that has been accepted. For A: GO analysis using topGO Arabidopsis
Commentator 4 months ago, created a comment with at least 3 up-votes. For C: Pheatmap error: 'gpar' element 'fill' must not be length 0 , what to do about
Appreciated 6 months ago, created a post with more than 5 votes. For A: GO analysis using topGO Arabidopsis
Scholar 6 months ago, created an answer that has been accepted. For A: GO analysis using topGO Arabidopsis
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: GO analysis using topGO Arabidopsis

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1408 users visited in the last hour