{"items": [{"url": "/p/123751/", "text": "org.Hs.eg.db can not be downloaded", "id": "/p/123751/", "context": "Hi, \r\nI can't download org.Hs.eg.db package with the language on \"org.Hs.eg.db bioconductor\" by R software type 3.6.1. The following is the discription when I run the R software. I will be appreciated...", "author": "betty888.wang"}, {"url": "/p/123751/#123752", "text": "A: org.Hs.eg.db can not be downloaded", "id": "/p/123751/#123752", "context": "The error message says 'load faild for 'AnnotationDbi'. Try loading it only\r\n\r\n```\r\nlibrary(AnnotationDbi)\r\n```\r\n\r\nand try to understand the error it reports...", "author": "Martin Morgan"}, {"url": "/p/123746/", "text": "DEseq2 analysis time-series data under two conditions", "id": "/p/123746/", "context": " I have time series data from two condition, like 0h, 2h, and 6h by treatment A and B. I want to know FDR different between A and B at 1h fold change for example compared with their individual 0h. in ...", "author": "Cindy"}, {"url": "/p/123746/#123747", "text": "A: DEseq2 analysis time-series data under two conditions", "id": "/p/123746/#123747", "context": "Please first take a look at the time series example in the DESeq2 workflow.", "author": "Michael Love"}, {"url": "/p/123491/#123718", "text": "A: vcountPDict fails on PDict", "id": "/p/123491/#123718", "context": "Hi Aditya,\r\n\r\nMaybe you were looking at the wrong man page. `vcountPDict()` is a generic function with dispatch on the 2nd argument (`subject`):\r\n```\r\nlibrary(BSgenome)\r\nvcountPDict\r\n# standardGeneric...", "author": "Herv\u00e9 Pag\u00e8s"}, {"url": "/p/123745/", "text": "Research Associate in statistical modelling", "id": "/p/123745/", "context": "         \r\n        Hello,\r\n         \r\n      I have interval censored data with some late-entry subjects and I'd like to estimate the Survival function. \r\n       Does the Icens package take into accoun...", "author": "fabiana.gordon"}, {"url": "/p/123744/", "text": "CDF not found", "id": "/p/123744/", "context": "Hello, I'm having a problem with Affymetrix array for Clariom S Rat\r\n\r\nWhen i run I get the follow error: \r\n\r\nlibrary(affy)\r\ndata <- ReadAffy() \r\neset <- affy::rma(data)\r\n\r\n\r\nError in getCdfInfo(objec...", "author": "ijvechetti"}, {"url": "/p/123743/", "text": "The correct specification of the model matrix to ComBat", "id": "/p/123743/", "context": "When using the ComBat function for batch correction, what is the difference between the following two specifications of the matrix model :\r\n\r\n    mod <- model.matrix(~1, dat=colData)\r\n    mod <- model...", "author": "Samuel"}, {"url": "/p/123742/", "text": "Using WGCNA for purposes other than RNA-SEQ/Microarray", "id": "/p/123742/", "context": "HI, \r\n\r\nI have recently used the WGCNA for a whole brain imaging experiment and it seems to have worked well, but I have a question. First some background:\r\nThe experiment consisted of imaging whole b...", "author": "Antonio.Aubry"}, {"url": "/p/123739/", "text": "DESeq2 - Comparing RNA-Seq and Ribo-Seq", "id": "/p/123739/", "context": "I'm attempting to compare total RNA-seq with Ribo-Seq, to determine if changes in Ribo-Seq are due to changes in transcriptional expression (akin to the analysis performed by Anota2Seq). I am, however...", "author": "timjoncooper"}, {"url": "/p/123731/", "text": "Can't install Genesis", "id": "/p/123731/", "context": "I have difficulty installing the Genesis package. Please kindly advise. \r\n\r\n> BiocManager::install(\"GENESIS\") \r\nBioconductor version 3.9 (BiocManager 1.30.4), R 3.6.0 (2019-04-26)\r\nInstalling package(...", "author": "winstondunnmd"}, {"url": "/p/123731/#123736", "text": "A: Can't install Genesis", "id": "/p/123731/#123736", "context": "There doesn't seem to be any errors here, the installation of GENESIS looks like it worked fine.  \r\n\r\nIf you're worried by the part that says:\r\n\r\n>  installation path not writeable, unable to update p...", "author": "Mike Smith"}, {"url": "/p/95695/", "text": "New function lfcShrink() in DESeq2", "id": "/p/95695/", "context": "I&#39;ve received a couple questions from users about why I moved the shrinkage of log2 fold changes from the DESeq() to the lfcShrink() function. Here&#39;s my answer I give in the vignette:\r\n\r\n&quot...", "author": "Michael Love"}, {"url": "/p/123733/", "text": "Sai Nikhith Cholleti ", "id": "/p/123733/", "context": "how can i convert rpkm values into raw read counts.Is there any function or package in R to do this. ", "author": "sainikhith508001"}, {"url": "/p/118056/", "text": "ChIPQC gives Bam file has 297 contigs Error: subscript contains out-of-bounds indices", "id": "/p/118056/", "context": "I like to use ChIPqc packages, so I used output of Bowtie2 (after deduplicating using Picards) as `Bam` file and used `narrowPeak` file as output of MACS2, but I faced with below Error.\r\n\r\n\r\n    sampl...", "author": "star"}, {"url": "/p/118056/#123727", "text": "A: ChIPQC gives Bam file has 297 contigs Error: subscript contains out-of-bounds in", "id": "/p/118056/#123727", "context": "After some research, I think I've found the cause of this bug. In ChIPQC:::sampleQC function, there is code to check for read length with the first 1000 reads of the first chromosome. Code follows:\r\n\r...", "author": "zhenfeng.liu1"}, {"url": "/p/123716/", "text": "Research Associate in statistical modelling", "id": "/p/123716/", "context": "I have interval censored data with some late-entry subjects. Does the Icens package supports left truncation and if so could you give and example?\r\n\r\n", "author": "fabiana.gordon"}, {"url": "/p/123709/", "text": "getBSgenome{Bsgenome}: avoid attaching BiocGenerics (and others)", "id": "/p/123709/", "context": "Is there a way to avoid BiocGenerics, S4Vectors, IRanges, and Biostrings from being attached when calling BSgenome::getBSgenome() ?\r\n\r\n    bsgenome <- BSgenome::getBSgenome('mm10')\r\n\r\n    Attaching pa...", "author": "Aditya"}, {"url": "/p/123696/", "text": "Can't install TopmedPipeline Package", "id": "/p/123696/", "context": "I am a student of SISG Module 17. We learned about the TopmedPipeline functions during the module. This is an extremely useful package but I have only been able to run this through the DataStage and n...", "author": "winstondunnmd"}, {"url": "/p/123696/#123706", "text": "A: Can't install TopmedPipeline Package", "id": "/p/123696/#123706", "context": "This support site is for Bioconductor maintained packages.  TopmedPipeline is not a Bioconductor maintained package and you might have better luck on [StackOverflow](https://stackoverflow.com/)  or [B...", "author": "shepherl"}, {"url": "/p/123659/", "text": "Is the colnames of model.matrix on the page 34 in edgeR User's Guide?", "id": "/p/123659/", "context": "Hi Gordon Smyth and other authors of edgeR,\r\nIt seemed that the colnames of design2 on page 34 in edgeR User's Guide were wrong. They should be (intercept), groupA and groupB, not  (intercept), groupB...", "author": "2002ymx02"}, {"url": "/p/123659/#123705", "text": "A: Is the colnames of model.matrix on the page 34 in edgeR User's Guide?", "id": "/p/123659/#123705", "context": "Yes, you are right. Thanks for alerting us. Now fixed.", "author": "Gordon Smyth"}, {"url": "/p/117119/", "text": "Oligo RMA normalization : ERROR; return code from pthread_create() is 22", "id": "/p/117119/", "context": "I am trying to use oligo::rma for a HTA feature set from a linux environment and right after background correction, following is trace back \u2013 \r\nBackground correcting\r\n\r\n    Error in basicRMA(pms, pnVe...", "author": "RV"}, {"url": "/p/122925/", "text": "Minfi issue:  return code from pthread_create() is 22", "id": "/p/122925/", "context": "I went to estimate cell counts from a 450k RGSet with \r\n```\r\n    estimateCellCounts(RGSet, referencePlatform = c(\"IlluminaHumanMethylation450k\"))\r\n```\r\nI got the following:\r\n```\r\n> cellCounts <- estim...", "author": "jshouse"}, {"url": "/p/117119/#123061", "text": "A: Oligo RMA normalization : ERROR; return code from pthread_create() is 22", "id": "/p/117119/#123061", "context": "I struggled with the same error with `oligo` and `affy` for the past few days, resulting in a loss of not so insignificant amount of hair.\r\n\r\nThe error occurs in `libpthread.so`, one of the shared lib...", "author": "jdshih"}, {"url": "/p/122925/#123062", "text": "A: Minfi issue:  return code from pthread_create() is 22", "id": "/p/122925/#123062", "context": "I had the same error using `oligo` and `affy`, and the source of the error appears to be `openblas >= 0.3.4`.\r\nYou can see in your R session history that you are using `openblas 0.3.5`.\r\n\r\nFor now, I'...", "author": "jdshih"}, {"url": "/p/123027/", "text": "Deciphering Wilkinson Notation and Predictor Variables", "id": "/p/123027/", "context": "Trying to understand how to make the correct design for DESeq. [This very nice website][1] deciphers the notation for me, but I have no idea on how to interpret the predictor variables. After some fru...", "author": "dennism9251"}, {"url": "/p/123027/#123029", "text": "A: Deciphering Wilkinson Notation and Predictor Variables", "id": "/p/123027/#123029", "context": "As part of PH525 at Harvard, Rafa and I made this lecture series. See \u201cInteractions and contrasts\u201d\r\n\r\nhttps://genomicsclass.github.io/book/", "author": "Michael Love"}, {"url": "/p/113077/", "text": "pathview: object 'bods' not found", "id": "/p/113077/", "context": "I use pathfindR package and find a problem related to pathview package.\r\nError in pathview::pathview(gene.data = gene_data, gene.idtype = &quot;SYMBOL&quot;,  : \r\n  object &#39;bods&#39; not found\r\nIn...", "author": "Shi-Xiang Wang"}, {"url": "/p/113077/#122997", "text": "A: pathview: object 'bods' not found", "id": "/p/113077/#122997", "context": "As per [here][1], this is a common issue and usually can be solved by unloading and loading the package:\r\n```\r\ndetach(\"package:pathfindR\", unload=TRUE)\r\ndetach(\"package:pathview\", unload=TRUE)\r\nlibrar...", "author": "anamaria"}, {"url": "/p/123067/", "text": "Contrast vs relevel (DESEq2)", "id": "/p/123067/", "context": "Hello everyone, \r\n\r\nFrom the vignette of DESeq2, I can either set the factor level by doing this code\r\n\r\n    dds= relevel(dds$condition, ref=\u201cuntreated\u201d)\r\n\r\nOr I can use the contrast,\r\n\r\n    res <- re...", "author": "Merlin "}, {"url": "/p/123067/#123069", "text": "A: Contrast vs relevel (DESEq2)", "id": "/p/123067/#123069", "context": "You can have zero counts in two groups when there are more than two groups.", "author": "Michael Love"}, {"url": "/p/123058/", "text": "DESeq2 more than 2 groups comparison", "id": "/p/123058/", "context": "Hello, \r\n\r\nI am new to DE analysis, and I also looked for the answer to my question prior to writing, so sorry if there is a similar thread already and I couldn't find it.\r\n\r\nI am trying to analyze th...", "author": "sstankovic"}, {"url": "/p/123060/", "text": "collapseReplicates changes the order of the original dataframe in DESeq2", "id": "/p/123060/", "context": "Hi all,\r\n\r\nI noticed a strange behaviour of `collapseReplicates` function of DESeq2 v 1.22.2.\r\nAfter collapsing replicates, DESeq2 for some reorders the columns in the dataframe. Below is an example:\r...", "author": "gtechbio"}, {"url": "/p/123060/#123064", "text": "A: collapseReplicates changes the order of the original dataframe in DESeq2", "id": "/p/123060/#123064", "context": "The `dds` is output in the order of the grouping factor (e.g. the sample ID) that was used to perform the collapsing operation. You can re-order as you like after collapsing, e.g.:\r\n\r\n```\r\ndds <- dds[...", "author": "Michael Love"}, {"url": "/p/123058/#123065", "text": "A: DESeq2 more than 2 groups comparison", "id": "/p/123058/#123065", "context": "This is one of the frequently asked questions in the vignette (see FAQ at the end).", "author": "Michael Love"}, {"url": "/p/123040/#123045", "text": "A: DEseq2 ncol(countData) == nrow(colData) is not TRUE Error", "id": "/p/123040/#123045", "context": "You can probably debug this on your end. The counts matrix needs to have same number of columns as the sample table (colData) has rows, because columns of the counts matrix are matched with samples (t...", "author": "Michael Love"}, {"url": "/p/123042/", "text": "deseq2 correction batch effect without design", "id": "/p/123042/", "context": "Hi\r\n\r\nI would like to correct batch effect using deseq2, to analyze one hundred of RNA-Seq of tumors, without experimental design. 80 tumors were sequenced in 2018, and 20 in 2019; I can see a strong ...", "author": "mdidish"}, {"url": "/p/123042/#123044", "text": "A: deseq2 correction batch effect without design", "id": "/p/123042/#123044", "context": "DESeq does not correct the batch effect, it incorporates it into its linear model making.  And you do that just like above, by adding batch to the design along with the other elements of the experimen...", "author": "swbarnes2"}, {"url": "/p/122976/", "text": "Feedback on edgeR model setup: identifying sex-by-tissue effects", "id": "/p/122976/", "context": "I have RNA-seq data from 5 males and 5 females for 4 tissue types (skin, liver, brain, and gonads), and I would like to:\r\n1. Identify genes/transcripts with skin-biased expression\r\n2. Identify genes/t...", "author": "spflanagan.phd"}, {"url": "/p/122976/#123037", "text": "A: Feedback on edgeR model setup: identifying sex-by-tissue effects", "id": "/p/122976/#123037", "context": "You don't mention whether the samples from different tissues are collected from the same set of 5 males and 5 females. I'm going to assume that each set of samples for a particular tissue was collecte...", "author": "Aaron Lun"}, {"url": "/p/123032/#123034", "text": "A: SNP Flanking Seq ", "id": "/p/123032/#123034", "context": "For the first question, you will use the GenomicRanges package and a package or other source with relevant reference genome, e.g., \r\n\r\n    library(GenomicRanges)\r\n    library(\"BSgenome.Hsapiens.UCSC.h...", "author": "Martin Morgan"}, {"url": "/p/123032/", "text": "SNP Flanking Seq ", "id": "/p/123032/", "context": "Two queries:\r\ni. What is the package in Bioconductor where the position of a SNP can be specified to get its flanking sequences?\r\nii. What is the way to highlight or put brackets around a nucleotide a...", "author": "prodhan82"}, {"url": "/p/123057/", "text": "ASpli package function plotGenomicRegions fails in windows", "id": "/p/123057/", "context": "Dear all\r\n\r\nI am using the following function in ASpli package:\r\n\r\n    mm10 <- TxDb.Mmusculus.UCSC.mm10.knownGene\r\n    features <- binGenome(mm10)\r\n\r\n    targetssmall <- cbind(c( \"257101.bam\",\"258113....", "author": "mgdrnl"}]}