User: eleonoregravier

Reputation:
40
Status:
New User
Location:
France
Last seen:
1 month, 1 week ago
Joined:
3 years, 1 month ago
Email:
e**************@hotmail.com

Posts by eleonoregravier

<prev • 27 results • page 1 of 3 • next >
0
votes
3
answers
135
views
3
answers
Answer: A: sample size determination in microarrays studies with limma analysis
... Thanks a lot Aaron for your detailed answer. The idea here is to simulate a dataset with the same caracteristics than the pilot dataset and to increase the sample size to reach the desired number of significant genes. I do not understand all your computations but I have some questions : - Does th ...
written 3 months ago by eleonoregravier40
4
votes
3
answers
135
views
3
answers
sample size determination in microarrays studies with limma analysis
... Hi BioC community, I study the gene expression profiles of three groups by microarray data. The aim is to perform the pairwise comparisons of the three groups. The sample size of each of the group is n=10. GCRMA normalization and filtering were applied before using limma to perform differential an ...
0
votes
1
answers
175
views
1
answers
Comment: C: Different microarrays annotations provided by toTable and annotateEset functions
... Thanks a lot James for your very clear answer. I understand that the current way to annotate microarrays is to return all one-to-many mappings (return just the first mapped value). However, I dont understand very well why it is recommended to return all one-to-many mappings comparing to what was do ...
written 6 months ago by eleonoregravier40
1
vote
1
answer
175
views
1
answer
Different microarrays annotations provided by toTable and annotateEset functions
... Hi BioC community, I work on transcriptomic data from the GeneChip Human Gene 2.1 ST Array (Affymetrix). Up to now, I used the toTable function from AnnotationDbi package to get the entrez_id of each probe_id : library(AnnotationDbi) library(hugene21sttranscriptcluster.db) entrezidHugene <- ...
microarray annotation affycoretools annotationtools annotationdbi written 6 months ago by eleonoregravier40 • updated 6 months ago by James W. MacDonald46k
0
votes
3
answers
958
views
3
answers
Comment: C: Batch with only one sample or condition
... I understand what you say for batches 5 and 6 but for the other batches (batch 2 and 3 for example), there is not necessary the 2 samples from the same patient in the same batch... so not take into account batch effect is not correct because differences within a patient can be due to batch effect.   ...
written 2.6 years ago by eleonoregravier40
0
votes
3
answers
958
views
3
answers
Comment: C: Batch with only one sample or condition
... Hi again, The last samples (batches B5 and B6) are not yet processed in spectrometry. I think it would be possible to ask for processing again some of the samples already processed in batches B1 to B4 within the batches B5 and B6. It could simply "save" these samples but I am wondering if it could ...
written 2.6 years ago by eleonoregravier40 • updated 2.6 years ago by Gordon Smyth34k
0
votes
3
answers
958
views
3
answers
Comment: C: Batch with only one sample or condition
... Thanks al lot Gordon and Aaron for your valued help Eléonore ...
written 2.6 years ago by eleonoregravier40
0
votes
3
answers
958
views
3
answers
Comment: C: Batch with only one sample or condition
... Dear Aaron and svlachavas, Thanks for your quick answers. If I well understand, Aaron recommends to use the two following approaches and see what happens : design <- model.matrix(~0+batch+Treat) and patient in duplicateCorrelation design <- model.matrix(~0+Treat) and batch in duplicateCorr ...
written 2.6 years ago by eleonoregravier40 • updated 2.6 years ago by Ryan C. Thompson6.8k
7
votes
3
answers
958
views
3
answers
Batch with only one sample or condition
... Hi BioC community, I have proteomic data for 2 conditions A and B. 15 patients are included in A group and 40 patients in B group. The proteome of each patient was measured at time 0 (before treatment) and time 22 (after treatment). So we study 110 samples, corresponding to 55 patients (2 samples b ...
limma batch effect written 2.6 years ago by eleonoregravier40 • updated 2.6 years ago by Gordon Smyth34k
0
votes
1
answers
873
views
1
answers
Comment: C: limma with continous covariate depending on gene, 2 block variables, pairing and
... Yes, it will safer ! ...
written 2.7 years ago by eleonoregravier40

Latest awards to eleonoregravier

Popular Question 13 months ago, created a question with more than 1,000 views. For Statistical analysis of Spectral count data : edgeR, limma or others ?
Popular Question 16 months ago, created a question with more than 1,000 views. For batch effect : comBat or blocking in limma ?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 210 users visited in the last hour