User: A

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Posts by A

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Comment: C: DESeq2 multiple group comparison
... Thank you I done so > head(meta) IC PD.L1 TC TILs TILs.group A1 3 1 3 0 2 B1 2 1 0 0 1 C1 2 1 0 0 2 D1 0 0 0 0 2 E1 1 0 0 1 3 F1 0 0 0 0 1 > ...
written 2 days ago by A3.5k
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Comment: C: DESeq2 multiple group comparison
... Sorry Kevin I am confused with data I have, can you please have a look I have gene expression raw counts like this A1 B1 C1 D1 E1 F1 A2M 511 1623 665 208 553 469 AADAT 34 137 372 7 52 124 ABCB1 119 114 123 22 25 89 ABCB11 27 186 200 ...
written 3 days ago by A3.5k
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Comment: C: Summing up prob level
... @Kevin you thought me `limma::avereps` function in my previous query if not I was wandering in google without getting the answer Thank you ...
written 5 days ago by A3.5k
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Answer: A: Summing up prob level
... > limma::avereps(array,ID=rownames(array)) ...
written 6 days ago by A3.5k
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Summing up prob level
... Hi I have normalized a microarray data and matched the prob identifiers to gene symbol but now for some genes I have several probes. For example for gene A I have several matched probes. So I have repetition for gene A. How I can take mean over the expression of repeated genes please and having an ...
gene R microarray written 6 days ago by A3.5k
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Comment: C: Microarray Probes to Ensembl ID or Gene ID - clariomdhumanprobeset.db
... Sorry Kevin I have Rosetta probe identifiers I have a Agilent microarray gene expression matrix like this by weird gene IDs in rows. > head(mat[1:10,1:5]) GSM482796 GSM482797 GSM482798 GSM482799 GSM482800 10019475365 0.243 0.0176 0.1200 0.0994 0.0782 ...
written 13 days ago by A3.5k
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Comment: C: Normalization agilent microarray data?
... Thank you your code gave me > Is this matrix normalized now? I am not sure which accession are in rows :( and how I could gene symbol instead ...
written 14 days ago by A3.5k
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Comment: C: Normalization agilent microarray data?
... Sorry Kevin I perused your answer here and I finished with something names gset with class of Expressionset but I don't know how to get normalized matrix for `` GEO accession through this code Actually the ultimate goal is a survival Kaplan meier plot for this list of genes for this data sets ...
written 14 days ago by A3.5k
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Comment: C: Sample outlier detection in DESeq2
... Sorry Kevin We have raw read counts from sequencing using a technique that only sequence 1402 immune related genes (HTG) I used DESeq2 and I am seeing my samples are too disperse ![enter image description here][1] [1]: https://i.ibb.co/0Z599rF/Rplot01.png And as you are seeing in this link ...
written 27 days ago by A3.5k
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Comment: C: Volcano Plot from DEseq2
... Sorry Kevin By these lines I plotted the volcano FC <-0.5 p <- 0.05 keyvals <- rep('grey75', nrow(res_responders)) names(keyvals) <- rep('NS', nrow(res_responders)) keyvals[which(abs(res_responders$log2FoldChange) > FC & res_responders$pvalue > p)] <- ' ...
written 5 weeks ago by A3.5k

Latest awards to A

Scholar 6 days ago, created an answer that has been accepted. For A: converting LOC to prpbset ID
Popular Question 10 days ago, created a question with more than 1,000 views. For taking intersection between two networks
Appreciated 10 days ago, created a post with more than 5 votes. For A: R - removing column names from matrix
Popular Question 10 days ago, created a question with more than 1,000 views. For taking intersection between two networks
Popular Question 12 days ago, created a question with more than 1,000 views. For taking intersection between two networks
Popular Question 5 weeks ago, created a question with more than 1,000 views. For taking intersection between two networks
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: using featureCounts in command line
Popular Question 6 weeks ago, created a question with more than 1,000 views. For extracting differential expressed genes from limma
Great Question 6 weeks ago, created a question with more than 5,000 views. For error in R when installing DESeq2 package
Popular Question 6 weeks ago, created a question with more than 1,000 views. For extracting differential expressed genes from limma
Popular Question 8 weeks ago, created a question with more than 1,000 views. For extracting differential expressed genes from limma
Popular Question 9 weeks ago, created a question with more than 1,000 views. For extracting differential expressed genes from limma
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: using featureCounts in command line
Popular Question 3 months ago, created a question with more than 1,000 views. For significant differential expressed gene validation
Popular Question 3 months ago, created a question with more than 1,000 views. For only a few differential expressed genes
Popular Question 3 months ago, created a question with more than 1,000 views. For extracting differential expressed genes from limma
Popular Question 3 months ago, created a question with more than 1,000 views. For only a few differential expressed genes
Popular Question 3 months ago, created a question with more than 1,000 views. For significant differential expressed gene validation
Popular Question 3 months ago, created a question with more than 1,000 views. For only a few differential expressed genes
Popular Question 3 months ago, created a question with more than 1,000 views. For only a few differential expressed genes
Popular Question 4 months ago, created a question with more than 1,000 views. For only a few differential expressed genes
Great Question 4 months ago, created a question with more than 5,000 views. For error in R when installing DESeq2 package
Great Question 4 months ago, created a question with more than 5,000 views. For error in R when installing DESeq2 package
Popular Question 4 months ago, created a question with more than 1,000 views. For format of data for enrichr
Popular Question 4 months ago, created a question with more than 1,000 views. For gene regulatory network visualization

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