User: eleonoregravier

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France
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1 month ago
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Posts by eleonoregravier

<prev • 25 results • page 1 of 3 • next >
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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 weeks ago by eleonoregravier40
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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 weeks ago by eleonoregravier40 • updated 6 weeks ago by James W. MacDonald45k
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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 2.2 years ago by eleonoregravier40
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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 2.2 years ago by eleonoregravier40 • updated 2.2 years ago by Gordon Smyth32k
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Comment: C: Batch with only one sample or condition
... Thanks al lot Gordon and Aaron for your valued help Eléonore ...
written 2.2 years ago by eleonoregravier40
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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 2.2 years ago by eleonoregravier40 • updated 2.2 years ago by Ryan C. Thompson6.3k
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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 2.2 years ago by eleonoregravier40 • updated 2.2 years ago by Gordon Smyth32k
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Comment: C: limma with continous covariate depending on gene, 2 block variables, pairing and
... Yes, it will safer ! ...
written 2.3 years ago by eleonoregravier40
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Comment: C: limma with continous covariate depending on gene, 2 block variables, pairing and
... OK for T1. Are you OK with my computation of treatment effect and sequence effect in the previous comment ? Thank very much for having spent time on my problem Eleonore   ...
written 2.3 years ago by eleonoregravier40
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Comment: C: limma with continous covariate depending on gene, 2 block variables, pairing and
... Hi Aaron, Thanks again for your help. I understand the part with gp.site where the reference level is T1 to explain evolution in different combinations treatment/time/site. For example treatment effect can be computed by substracting the mean from all the "NT" coefficients (4 terms) to the mean from ...
written 2.3 years ago by eleonoregravier40

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Popular Question 11 months ago, created a question with more than 1,000 views. For batch effect : comBat or blocking in limma ?

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