User: Andreia Fonseca

gravatar for Andreia Fonseca
Reputation:
810
Status:
Trusted
Location:
Last seen:
2 years, 8 months ago
Joined:
9 years, 11 months ago
Email:
a**************@gmail.com

Posts by Andreia Fonseca

<prev • 83 results • page 1 of 9 • next >
0
votes
3
answers
500
views
3
answers
Answer: A: cellHTS2 importa and analysing data from chemical compound screening
...   Dear Joseph, thanks so much for your reply. The platelist file is tab delimited but I will check if there is ay bug regarding that. The condition column should be the first? It is not in the example provided. With kind regards, Andreia     ...
written 2.9 years ago by Andreia Fonseca810
2
votes
3
answers
500
views
3
answers
cellHTS2 importa and analysing data from chemical compound screening
...     Dear Forum, I am analysing  data from a chemical screen (~3000 compounds spread over plates of 96 wells) which was performed in different cell lines, and within a cell line I am studying 3 conditions, WT, Mut1, Mut2. But no replicates are available for most of the plates. Each time a plate is ...
cheminformatics cellhts2 written 2.9 years ago by Andreia Fonseca810 • updated 2.9 years ago by Joseph Barry160
0
votes
0
answers
734
views
0
answers
test qPCR data for differential expression
... Dear all, I have to test for differential expression some qPCR experiments made for 7 genes. I am using the Delta Cts and I am fitting a linear model to acess if cell type (2 levels) has a significant effect in gene expression. I would like to understand the results that I m getting. When testing ...
qpcr written 6.3 years ago by Andreia Fonseca810
0
votes
1
answer
1.3k
views
1
answers
Comment: C: htseq and dexseq
... dear Simon, thanks for your reply, now its more clear what is happening. My issue was that even discarding the reads of the gene fusions, the total of counts of the exons was still much higher that the total number of reads aligned, now I understand from your reply and Steven that this will occurs ...
written 6.3 years ago by Andreia Fonseca810
0
votes
1
answer
1.3k
views
1
answers
Comment: C: htseq and dexseq
... Hi, You are right these cases are the minority. My feelling was to leave these apart but I was affraid to be discarding something important. Thanks for the tips. Kind regards, Andreia Sent from my iPad On 26/06/2013, at 22:56, Steve Lianoglou wrote: > Hi, > > On Wed, Jun 26, 2013 at ...
written 6.3 years ago by Andreia Fonseca810
0
votes
1
answer
1.3k
views
1
answers
Comment: C: htseq and dexseq
... here is an attach with the summary of the counts I sent On Wed, Jun 26, 2013 at 10:00 PM, Andreia Fonseca wrote: > Thanks Steve, > > The vignette looks very useful. ;y question was not related with counting > into two exons of same gene. With Htseq we get counts for exons that > o ...
written 6.3 years ago by Andreia Fonseca810
0
votes
1
answer
1.3k
views
1
answers
Comment: C: htseq and dexseq
... Thanks Steve, The vignette looks very useful. ;y question was not related with counting into two exons of same gene. With Htseq we get counts for exons that overlap different genes, so it creates feature fusing two or more genes, and I don't know how to handle this. should I look into the counts of ...
written 6.3 years ago by Andreia Fonseca810
0
votes
1
answer
1.3k
views
1
answer
htseq and dexseq
... Dear all, sorry if this question is not appropriate to this list, but if you are using DEXSeq probably you used htseq to make exon count previously. While making the counts using the python script available we saw that counts are being attributted to regions overlaping 2 genes, that what we think i ...
dexseq written 6.3 years ago by Andreia Fonseca810 • updated 6.3 years ago by Steve Lianoglou12k
0
votes
1
answer
932
views
1
answer
nsfilter error from expressionset obtained after using aroma for processing
... Dear all, I am analyzing data obtained using the HuGene2.0-st arrays from affymetrix. I have used aroma for preprocessing and limma for diff. expression analysis. After multiple testing I lost significance and therefore I want to filter out genes that do not have a potential to be significantly d ...
annotation preprocessing hgu95av2 limma written 6.5 years ago by Andreia Fonseca810 • updated 6.5 years ago by Wolfgang Huber13k
0
votes
1
answer
764
views
1
answer
xps- not being able to load it
... Dear Christian, thanks for the help I have followed your instructions and root is installed, I can start root from any directory, however I am still not being able to load xps on R, I am getting the same error (error message below) how can I setup the the lib folder on /usr/local/root/lib/root/li ...
xps written 6.5 years ago by Andreia Fonseca810 • updated 6.5 years ago by cstrato3.9k

Latest awards to Andreia Fonseca

Popular Question 2.7 years ago, created a question with more than 1,000 views. For problems in installing biomart
Popular Question 2.7 years ago, created a question with more than 1,000 views. For htseq and dexseq
Popular Question 2.7 years ago, created a question with more than 1,000 views. For fitting growth curve
Popular Question 2.7 years ago, created a question with more than 1,000 views. For getBM
Popular Question 2.7 years ago, created a question with more than 1,000 views. For installation of org.Hs.eg.db

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 171 users visited in the last hour