User: RNAseqer

gravatar for RNAseqer
RNAseqer 110
Reputation:
110
Status:
Trusted
Location:
Last seen:
1 week, 2 days ago
Joined:
5 months, 1 week ago
Email:
z*****@gmail.com

Very new to RNAseq, previous experience in genome assembly, phylogenetic analysis, substitution rate analysis etc etc.

Posts by RNAseqer

<prev • 71 results • page 1 of 8 • next >
0
votes
1
answer
101
views
1
answer
how to adjust for continuous covariates in limma?
... I'm fairly new to limma and just want to double check if I am doing something correctly. I have some microarray data and am looking for genes differentially expressed between states DIS and TE. I have several continuous covariates (V0, V1, V2 etc. in the phenotype data cov.tb) I am only intereste ...
de limma continuous covariates written 10 days ago by RNAseqer 110 • updated 10 days ago by i.sudbery5.0k
0
votes
0
answers
51
views
0
answers
summarized probes with expresso. how do i get transcript IDs?
... I just summarized a dataset using the expresso() function. I then normalized the data using limma's "normalizebetweenarrays()" function. But now I need to pull out just the miRNA data from everying else on the chip...and while i have a list of miRNA transcript names, I have rownames such as "14qI-8_ ...
transcript id affy expresso written 22 days ago by RNAseqer 110
0
votes
0
answers
92
views
0
answers
is there an function to summarize miRNA array probes but do nothing else?
... Hey I have an odd problem: I was using the oligo package to do RMA on some affy miRNA microarray data. It seems that the oligo package combines mutiple probes into one expression value automatically during the normalization process. Thats been great. Now I would like to do cyclic loess normali ...
summarise probes affy mirna written 4 weeks ago by RNAseqer 110
0
votes
0
answers
125
views
0
answers
Error "Bioconductor - mirna40cdf not available"
... Hello all, I need to compare the performance of RMA to mas5.0 normalization on some microarray data. This is not a matter of weighing the merits of rma against those of mas5, but rather seeing if a signal detected in rma normalized data is present when a different normalization technique, mas5.0 ...
affy mirna40cdf mirna written 5 weeks ago by RNAseqer 110
0
votes
0
answers
132
views
0
answers
Comment: C: changing feature names (row names) for expressionset object?
... Thanks! That is good to know. It seems as though this was fixed automatically a step or two later in the pipeline by the rma function. After rma the rownames do appear to be probe IDs again. ...
written 7 weeks ago by RNAseqer 110
0
votes
0
answers
120
views
0
answers
extracting a subset of probes from an expression object
... I have some normalized microarray data in an object generated by the following commands: > raw_data5 <- oligo::read.celfiles(filenames = "VV51m.CEL", "VV50m.CEL", ...) ...
probes exprs microarray subset written 7 weeks ago by RNAseqer 110
0
votes
0
answers
132
views
0
answers
Comment: C: changing feature names (row names) for expressionset object?
... > raw_data3 <- oligo::read.celfiles(filenames = "VV51m.CEL", "VV50m.CEL", ... ) ...
written 7 weeks ago by RNAseqer 110
2
votes
0
answers
132
views
0
answers
changing feature names (row names) for expressionset object?
... Hello everyone, Has anyone had experience changing the rownames of the expressionset (the intensity matrix) for an affy expression-set object? Somehow mine got changed from probe IDs to simple numbers (1 for the first probe, 2 for the second etc.) and I'd like to change them back. > exp ...
rownames expressionset limma written 7 weeks ago by RNAseqer 110
0
votes
0
answers
102
views
0
answers
whats is the best normalization technique for miRNA microarray data?
... Hello all, So I have some Affy microarray data for miRNAs and I'm wondering what normalization techniques to apply to it. As I understand it the challenges inherent in miRNA nomalization are, unlike mRNA: 1) the smaller number of miRNAs as opposed to mRNA means there is less to work with 2) t ...
normalization microarray mirna written 7 weeks ago by RNAseqer 110
0
votes
1
answer
133
views
1
answers
Comment: C: How to in R: Include principal components as covariates in analysis
... Hello Kevin, I'ts been a many years since I did anything with principal components and over the past few months I've done a lot of brushing up on the subject but I'm just having a bit of trouble understanding what some of their values are in the above covariate analysis. As I understand it PCA ...
written 8 weeks ago by RNAseqer 110

Latest awards to RNAseqer

Rising Star 11 weeks ago, created 50 posts within first three months of joining.
Supporter 11 weeks ago, voted at least 25 times.
Autobiographer 5 months ago, has more than 80 characters in the information field of the user's profile.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1927 users visited in the last hour