User: roser.navarro

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Posts by roser.navarro

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Comment: C: design microarrays limma
... Thanks a lot for your help! One more question... If I test the equal-variance hypothesis and we accept that they are equal, is my assumption, related to subsetting, right to avoid domination by the largest group?  We have to compare the variance within each group (considering all the genes), haven ...
written 6 weeks ago by roser.navarro0
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design microarrays limma
... Dear all, We are using limma to perform differential expression analysis among 3 different groups. The problem (or not) is that the design is unbalanced. The sample size per group is very different (7, 9 and 39 samples). So, we decided to do a random selection from the big group to balance the des ...
microarray limma design statistical power variability written 6 weeks ago by roser.navarro0 • updated 6 weeks ago by Aaron Lun17k
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combine two differential expression methods
... Dear all, We have done differential expression analyses using edgeR and DESeq2. Then we have kept the genes detected by both methods as differentially expressed, trying to be more restrictive or conservative in our findings. Would it be better to use only the DEGs detected with one method instead ...
edger deseq2 publish dea written 7 weeks ago by roser.navarro0 • updated 7 weeks ago by Aaron Lun17k
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edgeR normalisation which samples to include
... Our RNA-Seq design includes two variables: time (three points) and treatment (treatment vs. control). There are a total of 6 samples per group which have been balanced and randomized in two different sequencing runs. We want to compare the treatment groups vs. the control group for each time point ( ...
normalization edger samples comparisons written 7 weeks ago by roser.navarro0 • updated 7 weeks ago by Gordon Smyth32k
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Comment: C: getting sample size for RNAseq experiment
... Dear Maarten, I hope this scheme helps you :-)   Stage 1(time point 1) Patient: Biopsy: Zone A: RNA-Seq Zone B: RNA-Seq Zone C: RNA-Seq Liquid: Cells: RNA-Seq And the same scheme for 5 different stages.   I want to know the number of patients per stage that should be ...
written 21 months ago by roser.navarro0
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Comment: C: getting sample size for RNAseq experiment
... Dear Maarten, First of all thanks for your answer :-) We want to compare more than 2 groups. We would like to compare 5 groups/conditions. Our goal is to calculate the number of patients per condition that we should to include in our study.  We don't have technical replicated because the 3 biops ...
written 21 months ago by roser.navarro0
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getting sample size for RNAseq experiment
... Dear all, I've read some papers and vignettes related to calculate the sample size for RNAseq experiments. Iv'e also tried to use some tools as RNAseqPS, rnaseqpower, sspa but all of them work with 2 groups. I have a problem because in our experimental design we are comparing more than 2 groups. ...
sequencing rnaseqpower complex-design sample size sspa written 21 months ago by roser.navarro0 • updated 21 months ago by m.van_iterson20
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Comment: C: limma: within-array duplicates correlation
... Thank you :-) ...
written 21 months ago by roser.navarro0
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Comment: C: limma: within-array duplicates correlation
... Thanks a lot for your help. I hope this will be my last question :-) This is my code (for the 2 approaches) When I started the analysis I used the following code. But I didn't get any DEG.   x <-read.maimages(targets_all$FileName, source="agilent", green.only = TRUE) colnames(x$E) <- targe ...
written 21 months ago by roser.navarro0
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Comment: C: limma: within-array duplicates correlation
... Thanks a lot Aaron Lun. I'm using avereps before using duplicateCorrelation on patients. But I don't know which of both approaches would be better.  Results using spots or patients are very different. That's why I would like to know if the following code is correct: DUPS = 30 ## we have 30 probe ...
written 21 months ago by roser.navarro0

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