User: spriyansh29

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spriyansh2930
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Posts by spriyansh29

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Comment: C: Probability in Genomics
... Not really! Just figuring out how to get started? Any leads? ...
written 5 weeks ago by spriyansh2930
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Answer: A: How to handle multiple mapping of Gene-Symbols and Probe-ID in Micro-array Data
... ```# Merging``` ```annotated <- as.data.frame(annotated %>%``` ```group_by(Gene.symbol) %>%``` ```filter(across(c("logFC"), ~ n_distinct(sign(.)) == 1)) %>%``` ```summarise(across(c("logFC","P.Value","adj.P.Val","B","AveExpr","t"), mean), X = str_c(X, collapse= " | "),``` ```Gene.ti ...
written 4 months ago by spriyansh2930
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How to handle multiple mapping of Gene-Symbols and Probe-ID in Micro-array Data
... After, performing the differential analysis with ```limma```. After, mapping with the feature data, I have got the data frame as follows- ```FDR``` ```Probe_ID``` ```Gene.Symbol``` ```Gene.ID``` ```0.009``` ```1555272_at``` ```RSPH10B2///RSPH10B``` ```728194///222967``` ```0.007``` ```1557203_at` ...
data-frame R micro-array gene probe-id written 5 months ago by spriyansh2930
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Comment: C: Calculating Contrast Matrix in Limma for Differential Expression
... Hi! thank you, it worked. However, after running the testing with the following code ````cont.matrix <- makeContrasts(disease_vs_healthy = (Lesional+Non.Lesional+Peri.Lesional)-(Healthy.Volunteer),levels=design)```` ````fit2 <- contrasts.fit(fit, cont.matrix)```` ````fit2 <- eBayes(fit2 ...
written 5 months ago by spriyansh2930
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Comment: C: Calculating Contrast Matrix in Limma for Differential Expression
... Hi! Thanks for the quick reply, I have tried by removing the ````""```` but still got the same error Here is the ````design```` ````> design```` ```` Healthy Volunteer Lesional Non Lesional Peri-Lesional```` ````1 1 0 0 0```` ````2 ...
written 5 months ago by spriyansh2930
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Calculating Contrast Matrix in Limma for Differential Expression
... **About the sample**: There are 40 samples in which 10 samples are healthy controls and 30 samples are diseased (10 of type-1 + 10 of type-2 + 10 of type-3). I wish to perform differential expression analysis between the 30 diseased and 10 controls, i.e. 30_diseased_vs_10_control. The accession id o ...
R contrast-matrix limma deg micro-array written 5 months ago by spriyansh2930
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Does the expression data from GEO Series Matrix File(s) can directly be used with limma workflow
... I have to perform differential gene expression analysis using ````limma````. Can I use GEO Series Matrix File(s) (expression set) in the limma workflow (differential expression analysis) without actually extracting the expression set from raw ````.CEL```` files. As I can see that ````limma```` work ...
normalization rma micro-array limma R written 6 months ago by spriyansh2930 • updated 6 months ago by Kevin Blighe67k
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Comment: C: Differential Gene Expression Analysis with low biological replicates
... I am quite new to RNA-Seq so I followed tutorials from bioconductor's website.For DESeq2 I have used ````DESeq(dds)```` and ````DESeq(dds, test="LRT", reduced = ~ 1)````. For EdgeR I have used ````glmQLFTest(fit,coef="Group2")```` and ````glmLRT(fit,coef=""Group2"")````. The plots are [Heatmap with ...
written 6 months ago by spriyansh2930
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Answer: A: STAR error (segmentation fault) in Aligning reads
... It was a hardware constraint, as STAR requires a minimum of 30Gigs of RAM. ...
written 6 months ago by spriyansh2930
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Differential Gene Expression Analysis with low biological replicates
... I have two groups with 12 (6 + 6) samples that were generated from bulk-RNA-Seq experiments. While performing the differential expression analysis the adjusted-p-value came out to be 1 with both DESEQ2 (Wald, LRT) and EdgeR (Quasi-likelihood, LRT). After, skimming through a few posts and papers, I f ...
R ngs differential-expression rna-seq written 6 months ago by spriyansh2930 • updated 5 months ago by Biostar ♦♦ 20

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Student 12 months ago, asked a question with at least 3 up-votes. For Identification of Human Genes ?

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