User: ghk

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ghk0
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Posts by ghk

<prev • 116 results • page 1 of 12 • next >
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How to normalize Microarray expression data?
... I have a data frame "df" like following with Microarray expression Data (Affymetrix SNP 6.0 data):     S1 S2 S3 S4 S5 S6 S7 A1BG 6.429276339 6.338451158 6.333760753 6.419191996 6.503471181 6.329103499 6.211373601 A2BP1 6.379471 ...
normalization R bioconductor affymetrix microarrays written 12 days ago by ghk0 • updated 12 days ago by James W. MacDonald44k
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Comment: C: Why Differential expression results differ with edgeR and limma ?
... Dear Aaron, Thanks a lot for helping me out. I found the bug in my code. "counts" and "annot" samples were same but they are not in the same order. I fixed that now.  I found differential expressed genes in both the ways (edgeR and limma-voom) Thanks again !! ...
written 7 weeks ago by ghk0
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Comment: C: Why Differential expression results differ with edgeR and limma ?
... Ok  And how should I give "design matrix" if it looks like following? I'm every time confused in creating design matrix. Sample.ID   Grade S1     3 S2     2 S3     3 S4      2 S5     4 S6     3 ...
written 7 weeks ago by ghk0
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Comment: C: Why Differential expression results differ with edgeR and limma ?
... In limma and voom.....the "y" you used is after Normalization or estimateDip?   ...
written 7 weeks ago by ghk0
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Comment: C: Why Differential expression results differ with edgeR and limma ?
... Please try with this data.   S3 S1 S4 S2 S6 S7 S5 ENSG00000000003.13 5578 4300 4587 12247 3296 2532 6436 ENSG00000000005.5 0 3 5 1 0 1 0 ENSG00000000419.11 1681 669 1187 2149 600 161 ...
written 7 weeks ago by ghk0
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Comment: C: Why Differential expression results differ with edgeR and limma ?
... Dear Aaron, I have done the same two way analysis with some other data. With the first way (limma, Glimma, edgeR) there are no differential expressed genes. In this way the differential expressed genes with topTable function are based on adj.P.Val <= 0.05. Am I right?  With the second way (edg ...
written 7 weeks ago by ghk0
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Comment: C: Why Differential expression results differ with edgeR and limma ?
... Sorry its not EG2 and EG3....Its F2 and F3. I edited just now. The results I got is correct. ...
written 7 weeks ago by ghk0
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Why Differential expression results differ with edgeR and limma ?
... Hello, I have counts data with 366 samples as columns and more than 50k ensembl ids as rownames. The data is stored in a dataframe "U". Data looks like following:                                                    S1                S2                S3 ENSG00000000003.13            5745           ...
limma edger R differential gene expression written 7 weeks ago by ghk0
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Comment: C: decideTests error with edgeR package
... Dear Aaron, I have a doubt. With the same data I used limma, Glimma and edgeR for Differential expression (http://combine-australia.github.io/RNAseq-R/06-rnaseq-day1.html) But with the same comparison I found only one differentially expressed gene. In this process data will be transformed into Voom ...
written 7 weeks ago by ghk0
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Comment: C: decideTests error with edgeR package
... Thank you very much Aaron. I guess all my doubts are cleared now! Just one last check. tr <- glmTreat(fit, contrast=contrast.matrix, lfc=log2(1.2)) tab2 <- topTags(tr,n=Inf) keep <- tab2$table$FDR <= 0.05 write.csv(tab2$table[keep,], file="DE.csv") In the .csv file in total I have 1 ...
written 7 weeks ago by ghk0

Latest awards to ghk

Popular Question 8 months ago, created a question with more than 1,000 views. For Heatmap with error message: `x' must be a numeric matrix
Popular Question 17 months ago, created a question with more than 1,000 views. For Heatmap with error message: `x' must be a numeric matrix
Rising Star 18 months ago, created 50 posts within first three months of joining.

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