User: 1234anjalianjali1234

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Posts by 1234anjalianjali1234

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Comment: C: Design/contrast matrix for Multivariate experimental design in limma
... I was wondering, how could we make design matrix for the chip given below:   Sample_title Organism Geo protocol_1 Label_1 protocol_2 label_2 non_GM_D_vs_GM_A_Pinf_1 Fungus GSM200048 Treated_24h Cy3 Treated_24h Cy5 non_GM_D_vs_GM_A_water_1 Fungus GSM200049 Contr ...
written 3 months ago by 1234anjalianjali12340
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Comment: C: Design/contrast matrix for Multivariate experimental design in limma
... Hellow Smyth, Here are the answer to your questions: 1.  For using InSilicoDb package I was using an older version of R [R.3.2.3], but I am not aware of this that it is not applicable to two-color array. 2. The reason you are not finding those identifiers in GEO because I have changed the ID, if ...
written 3 months ago by 1234anjalianjali12340
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Comment: C: Design/contrast matrix for Multivariate experimental design in limma
... Sorry for the inconvenience, I am getting replies on Biostar, hope to get my solution there. Thank you ...
written 3 months ago by 1234anjalianjali12340
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Design/contrast matrix for Multivariate experimental design in limma
... Hellow,  I have four number of Two-color array chips (.gpr files/ genepix) with different time points, infecting organism and with dye swaps and some having biological replicate. it's getting complicated for me to make design/contrast matrix to find differential gene expression. I have done normal ...
microarray limma design and contrast matrix written 3 months ago by 1234anjalianjali12340 • updated 3 months ago by Gordon Smyth34k
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Comment: C: How to make contrast table to combine two conditions/treatments against another
... als not working same error.   ...
written 2.1 years ago by 1234anjalianjali12340
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Comment: C: How to make contrast table to combine two conditions/treatments against another
... hi @ Aaron Lun, actually I have done the same thing you suggest here but I am getting an error. My codes are:   > samples <- c(eset1$characteristics, eset$characteristics)   > samples <- as.factor(samples) >samples >design <- model.matrix(~0 + samples) >colnames(design ...
written 2.1 years ago by 1234anjalianjali12340
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design matrix for dge
... I am doing Cross-platform normalization and network-based data analysis of gene expression data to find out potential biomarker of cancer .I have merged 3 datasets without any treatment ( two of Affymetrix Human Genome U133A Array and one with Affymetrix Human Genome U133A Array plus 2, platform GPL ...
limma written 2.1 years ago by 1234anjalianjali12340 • updated 2.1 years ago by Gordon Smyth34k

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