User: amin.ghareyazi

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Posts by amin.ghareyazi

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Comment: C: different designs for finding DEG by limma
... Groups in samples are from 5 types of cancer. I didn't find any use for MDS plots. And you are right about number of pairwise comparisons. Actually I am more interested in finding DEG for No. 1 and 2. Third one will be used for some rare situations in my study. Can you help me at least for No. 1 and ...
written 6 weeks ago by amin.ghareyazi0
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different designs for finding DEG by limma
... Hi I have a normalized and batch effect removed microarray data. I have 5 groups of samples namely S1 to S5. I have to find differentially expressed genes in 3 conditions below: 1) one group vs remaining groups (for example S2 VS S1,S3,S4,S5) 2) differentially expressed genes across all 5 groups ...
limma design deg written 6 weeks ago by amin.ghareyazi0
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Comment: C: DESeq2 multiple group comparison (ANOVA) with batch effect
... thanks Michael. I understood your recommendation. I will do as exactly you said. just to mention, those heatmaps are exactly outputs of guideline codes and it is not in count scale. It is normalized. Those 10 samples have great impact on results. ...
written 8 weeks ago by amin.ghareyazi0
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Comment: C: DESeq2 one group vs multiple groups comparison in presence of batch effect
... thanks Michael. It helped a lot... ...
written 8 weeks ago by amin.ghareyazi0
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Comment: C: DESeq2 one group vs multiple groups comparison in presence of batch effect
... So I just need to switch conditions in this list to get my desired comparison? should I change reference level for comparisons other than condition 1? ...
written 8 weeks ago by amin.ghareyazi0
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DESeq2 one group vs multiple groups comparison in presence of batch effect
... Hi I have 5 groups and 3 levels of batches. This is my code: rna.o=DESeqDataSetFromMatrix(data,colD,design = ~projects+Subtypes) rna.d.pair=DESeq(rna.o,parallel = T) this is my resultsNames: resultsNames(rna.d.pair) [1] "Intercept" "projects_PACA.CA_vs_PACA.AU" "projects_PAEN. ...
deseq2 batch comparison written 8 weeks ago by amin.ghareyazi0 • updated 8 weeks ago by Michael Love25k
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Comment: C: DESeq2 multiple group comparison (ANOVA) with batch effect
... good point. thanks. but how can it find out which column of colD is batch and which is groups? ...
written 8 weeks ago by amin.ghareyazi0
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Comment: C: DESeq2 multiple group comparison (ANOVA) with batch effect
... I tried first two PCs. Three projects were completely distinguished. But ComBat() did an excellent job in removing batch effects and batches couldn't be observed. see this [plot][1]. I'm just wondering if DESeq2 can cope with batch effect like ComBat? [1]: https://drive.google.com/open?id=1kbPPy ...
written 8 weeks ago by amin.ghareyazi0
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Comment: C: DESeq2 multiple group comparison (ANOVA) with batch effect
... Final question: If I want to compare one group to multiple groups, I used this code: (for 2 VS 1,3,4,5) dds=DESeqDataSetFromMatrix(data,colD,design = ~projects+Subtypes) a=DESeq(dds) b=results(a,contrast = c(0,2,-1/4,-1/4,-1/4,-1/4,-1/4) ) Is it ok? ...
written 8 weeks ago by amin.ghareyazi0
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Comment: C: DESeq2 multiple group comparison (ANOVA) with batch effect
... What is your opinion on fourth plot? Do you think group 2 with only 10 samples (297 samples in other groups) can cause these significant p-values and batch effects have no role in this? ...
written 8 weeks ago by amin.ghareyazi0

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