User: tanyabioinfo

tanyabioinfo20
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Posts by tanyabioinfo

<prev • 22 results • page 1 of 3 • next >
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...   HI I am using the tximport module to process the output of Salmon. Then I am using the vst(dds) to normalise the data. I understand that the assay for dds is count. How can I process the abundance(TPM) using the vst so that my TPM data is normalised.  My R code looks: txi <- tximport(files, ...
written 6 months ago by tanyabioinfo20 • updated 6 months ago by Michael Love18k
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Comment: A: RNA seq tximport
... Hi Michael   Thanks a lot. My TPM data is showing a lot of variation in terms of trends than RPM. Like the tximport output gives a lot of  variation among the replicates. Can you please help me why this would be happening.   Thanks   Tanya ...
written 7 months ago by tanyabioinfo20
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... Hi I am using Salmon to process my RNA seq data. I just want to confirm that the abundance given as an output by the tximport package corresponds to TPM. Many of the cells (the output of tximport) have a value of zero which is making me think about this. Regards Tanya ...
written 7 months ago by tanyabioinfo20
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... Hi I am doing the following to get the tximport count  matrix with gene name in the first column txdf <- transcripts(EnsDb.Mmusculus.v79, return.type = "DataFrame") txdf$symbol <- mapIds(EnsDb.Mmusculus.v79, txdf$gene_id, "GENENAME", "GENEID") tx2gene <- as.data.frame(txdf[,c("tx_id","sym ...
written 7 months ago by tanyabioinfo20 • updated 7 months ago by Ed Siefker220
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Comment: A: PCA from TPM
... Hi Michael I am now using the follwoing code: txi <- tximport(files, type="salmon", tx2gene=tx2gene, ignoreTxVersion=TRUE,dropInfReps=TRUE) sampleTable <- data.frame(condition =samples$condition,time=factor(samples$time)) rownames(sampleTable) <- colnames(txi$counts) dds <- DESeqDataSe ... written 7 months ago by tanyabioinfo20 1 answer 266 views 1 answer ... Hi I am trying to do PCA analysis of my samples. I generated the matrix using the tximport package. I have transcript ids as my rows and the sample names are the columns. txi <- tximport(files, type="salmon", tx2gene=NULL, ignoreTxVersion=TRUE,dropInfReps=TRUE,txOut = TRUE) tpm <- (txi$abun ...
written 7 months ago by tanyabioinfo20
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... Thanks James It worked for me.   ...
written 7 months ago by tanyabioinfo20
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... Hi   I am using the following commands to run tximport txi <- tximport(files, type="salmon", tx2gene=tx2gene,ignoreTxVersion=TRUE,dropInfReps=TRUE) my tx2gene dataframe looks like this              tx_id            gene_id 1 ENSMUST00000082387 ENSMUSG00000064336 2 ENSMUST00000179436 ENSMUSG0 ...
written 7 months ago by tanyabioinfo20
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Comment: C: PCA plot for TPM data
... Thanks Andy. Can you please help me how can I add colors to this PCA plot based on sample names.   Thanks   Tanya ...
written 7 months ago by tanyabioinfo20
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... Hi I am having a TPM count matrix. The columns are the samples wt0hr wt6hr wt24hr kd0hr kd6hr kd24 and have four replicates for each one of them. Can some one help me with the correct R package to plot the PCA for samples when I have the TPM data.   Thanks Tanya ...
written 8 months ago by tanyabioinfo20 • updated 8 months ago by Andy9160

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