User: ea1402

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ea140220
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3 years ago
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4 years, 4 months ago
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Posts by ea1402

<prev • 16 results • page 1 of 2 • next >
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limma voom analysis with multiple comparisons
... Hi, I have an experiment where I have treated a cell line with two drugs A and B, their combination AB, as well as control C. So I have 4 treatments but also 3 time point time=3,9 and 24 hours. At each condition and time point i.e. A_3 I have 3 treatments. My goal is a dynamic analysis as such at e ...
limma voom written 3.1 years ago by ea140220 • updated 3.1 years ago by Aaron Lun25k
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limma complex design
... Hi, I have a complex design question with limma. We have 12 patients and we have several RNA seq data from each patient. PAtients have different sexes and race. From each patient we collected samples from different parts of the diseased and health tissues. So the idea is to see the heterogeneity of ...
limma voom written 3.8 years ago by ea140220 • updated 3.8 years ago by Gordon Smyth39k
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Comment: C: Limma Camera error
... the contrast.matrix1 has only one contrasts however, length(colnames(design))>2, still would be a problem? Updating bioconductor at the same time. ...
written 4.1 years ago by ea140220
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Comment: C: Limma Camera error
... > sessionInfo() R version 3.2.0 (2015-04-16) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 7 x64 (build 7601) Service Pack 1 locale: [1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C       ...
written 4.1 years ago by ea140220
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Comment: C: Limma Camera error
... I reinstalled limma without success. am I supposed to give input voom_data not voom_data$E? I am having more than 2 contrasts to compare I hope this does not cause any problems. ...
written 4.1 years ago by ea140220
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Comment: C: Limma Camera error
... Gordon thanks for helping I updated both R and bioconductor but issue is still there. Below is my complete code. I have 20 treatments and 9 control samples. so length(colnames(design))=21. So using camera in a for loop I am  checking all of the contrasts one by one as seen by the code: for (i in ...
written 4.1 years ago by ea140220
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Comment: A: Limma Camera error
... Thanks     ...
written 4.1 years ago by ea140220
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Limma Camera error
... Hi, I have done a differential expression analysis using limma. When I try the camera analysis  dummy_out=camera(voom_data,all_signatures_for_camera,design,contrast.matrix1) I get the error Error in U[iset, , drop = FALSE] : no 'dimnames' attribute for array Here the voom_data is the voom outpu ...
limma camera written 4.1 years ago by ea140220
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DE analysis with limma partial replicates
... I would like to analyze RNAseq with 6 conditions using limma/voom. I have 6 biological replicates for control, however for the other 5 conditions (say C1,C2,C3,C4,C5) I have no replicates. Ideally, I would like to do a variance estimation using the 6 replicates for the control, and using it compare ...
limma voom written 4.1 years ago by ea140220 • updated 4.1 years ago by Aaron Lun25k
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Deseq2 analysis with replicates only for control
... Hello all,   I am analyzing an RNAseq with 6 conditions using deseq2. I have 6 biological replicates for control, however for the other 5 conditions (say C1,C2,C3,C4,C5) I have no replicates. Ideally, I would like to do a variance estimation using the 6 replicates for the control, and using it com ...
deseq2 differential gene expression written 4.1 years ago by ea140220 • updated 4.1 years ago by Michael Love26k

Latest awards to ea1402

Popular Question 3.1 years ago, created a question with more than 1,000 views. For Limma Camera error
Popular Question 3.1 years ago, created a question with more than 1,000 views. For Log fold change on Limma

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